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Molecular Modeling for a Comparative Analysis of Interactions Between 2LTRZFP and 2-LTR-Circle Junctions. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10175-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Macedo-da-Silva J, Marinho CRF, Palmisano G, Rosa-Fernandes L. Lights and Shadows of TORCH Infection Proteomics. Genes (Basel) 2020; 11:E894. [PMID: 32764347 PMCID: PMC7464470 DOI: 10.3390/genes11080894] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/27/2020] [Accepted: 07/29/2020] [Indexed: 12/25/2022] Open
Abstract
Congenital abnormalities cause serious fetal consequences. The term TORCH is used to designate the most common perinatal infections, where: (T) refers to toxoplasmosis, (O) means "others" and includes syphilis, varicella-zoster, parvovirus B19, zika virus (ZIKV), and malaria among others, (R) refers to rubella, (C) relates to cytomegalovirus infection, and (H) to herpes simplex virus infections. Among the main abnormalities identified in neonates exposed to congenital infections are central nervous system (CNS) damage, microcephaly, hearing loss, and ophthalmological impairment, all requiring regular follow-up to monitor its progression. Protein changes such as mutations, post-translational modifications, abundance, structure, and function may indicate a pathological condition before the onset of the first symptoms, allowing early diagnosis and understanding of a particular disease or infection. The term "proteomics" is defined as the science that studies the proteome, which consists of the total protein content of a cell, tissue or organism in a given space and time, including post-translational modifications (PTMs) and interactions between proteins. Currently, quantitative bottom-up proteomic strategies allow rapid and high throughput characterization of complex biological mixtures. Investigating proteome modulation during host-pathogen interaction helps in elucidating the mechanisms of infection and in predicting disease progression. This "molecular battle" between host and pathogen is a key to identify drug targets and diagnostic markers. Here, we conducted a survey on proteomic techniques applied to congenital diseases classified in the terminology "TORCH", including toxoplasmosis, ZIKV, malaria, syphilis, human immunodeficiency virus (HIV), herpes simplex virus (HSV) and human cytomegalovirus (HCVM). We have highlighted proteins and/or protein complexes actively involved in the infection. Most of the proteomic studies reported have been performed in cell line models, and the evaluation of tissues (brain, muscle, and placenta) and biofluids (plasma, serum and urine) in animal models is still underexplored. Moreover, there are a plethora of studies focusing on the pathogen or the host without considering the triad mother-fetus-pathogen as a dynamic and interconnected system.
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Affiliation(s)
- Janaina Macedo-da-Silva
- Glycoproteomics Laboratory, Department of Parasitology, University of Sao Paulo, Sao Paulo 05508-000, Brazil;
| | - Claudio Romero Farias Marinho
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, University of Sao Paulo, Sao Paulo 05508-000, Brazil;
| | - Giuseppe Palmisano
- Glycoproteomics Laboratory, Department of Parasitology, University of Sao Paulo, Sao Paulo 05508-000, Brazil;
| | - Livia Rosa-Fernandes
- Glycoproteomics Laboratory, Department of Parasitology, University of Sao Paulo, Sao Paulo 05508-000, Brazil;
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, University of Sao Paulo, Sao Paulo 05508-000, Brazil;
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Silva CMD, Peder LDD, Thomazella MV, Teixeira JJV, Bertolini DA. PROFILE OF HCV GENOTYPES AND HIV-SUBTYPES AMONG HIV-COINFECTED PATIENTS IN SOUTHERN BRAZIL. ARQUIVOS DE GASTROENTEROLOGIA 2020; 56:344-350. [PMID: 31800733 DOI: 10.1590/s0004-2803.201900000-68] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 09/07/2019] [Indexed: 02/05/2023]
Abstract
BACKGROUND Hepatitis B and C virus (HBV and HCV) are the two most common infections among human immunodeficiency virus (HIV)-infected patients. OBJECTIVE To identify the frequency of HIV subtypes and HCV genotypes in HIV-coinfected patients. METHODS A cross-sectional and retrospective study was carried out into two reference centers in Southern Brazil between January 1, 2002 and June 30, 2016. The Abbott Real Time HCV Genotype II system was used for routine diagnostics to determine the HCV genotype based on dual-target real-time PCR. Proviral HIV-1 RNA was extracted from serum samples and fragments of the pol gene were generated by PCR. The HIV-1 PT and RT gene sequences were submitted to Maximum Likelihood Phylogenetic analysis by collecting reference sequences from the HIV-1 group M subtype of the Los Alamos database. RESULTS During the study period, 3340 patients with HIV were diagnosed at both referral centers, of which 4.97% (166/3340) had HBV and/or HCV coinfection. Seroprevalence of HIV-HBV, HIV-HCV and HIV-HBV-HCV was 37.4%, 58.4%, and 4.2%, respectively. HIV-HCV-coinfected patients had a lower median nadir CD4+ T-cell count when compared to HIV-HBV-coinfected patients (P=0.01). Among those coinfected with HCV, HCV-1 (HCV-1) and HCV-3 (HCV-3) genotypes were the most prevalent, being detected in 73.8% and 21.4%, respectively. Among the HCV-1 coinfected patients, 79.3% and 20.1% had subtypes 1a and 1b, respectively. HIV subtype B was the most prevalent in HIV-coinfected patients. There was no significant difference regarding nadir CD4+ T-cell count and HIV viral load when compared to coinfected with HCV-1 with HCV-3, as well as those co-infected with HCV-1a with HCV-1b. CONCLUSION In the present study, a higher frequency of subtype B of HIV and HCV-1 were found in HIV-coinfected patients. Further larger-scale and long-term studies are needed to better understand the effect of HCV genotypes in HIV-infected patients.
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Affiliation(s)
| | - Leyde Daiane de Peder
- Universidade Estadual de Maringá, Departamento de Análises Clínicas e Biomedicina, Maringá, PR, Brasil
| | - Mateus Vailant Thomazella
- Universidade Estadual de Maringá, Departamento de Análises Clínicas e Biomedicina, Maringá, PR, Brasil
| | | | - Dennis Armando Bertolini
- Universidade Estadual de Maringá, Departamento de Análises Clínicas e Biomedicina, Maringá, PR, Brasil
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Cravo LMDS, Biancardi AL, Ronconi TB, Xavier VL, Moraes H. Intraocular pressure in patients with human immunodeficiency virus, correlation with TCD4, viral load and demographic characteristics: a case-control study. Clin Ophthalmol 2019; 13:1477-1483. [PMID: 31496638 PMCID: PMC6689137 DOI: 10.2147/opth.s216759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 06/18/2019] [Indexed: 11/23/2022] Open
Abstract
Purpose To compare if patients with HIV have lower intraocular pressure than patients without HIV. Methods The association of intraocular pressure corrected by pachymetry and the relationship with viral load (VL) and TCD4 cells was studied. A total of 99 patients with HIV (91 who were on regular treatment and in control of the disease - group 1; and 8 who were without treatment - group 2) and 100 controls were studied. Results Only age was of statistical significance; the group with HIV without control of the disease was the youngest. There was a decrease of -1.54 mmHg in the IOP of group 1 in relation to the controls and -3.63 mmHg in the IOP of group 2 in relation to the controls. Conclusion HIV patients had lower IOP than the control population. However, the relationship between IOP, VL and TCD4 was not found.
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Affiliation(s)
- Leonardo Medlig de Sousa Cravo
- Postgraduate Surgical Sciences, Hospital Universitário da Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-590, Brazil
| | - Ana Luiza Biancardi
- Uveitis Ophthalmology Department, Hospital Universitário da Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-590, Brazil
| | - Thamiles Batista Ronconi
- Dermatology, Hospital Universitário da Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-590, Brazil
| | - Vinicius Layter Xavier
- Statistics Department, Institute of Mathematics and Statistics, Universidade Estadual do Rio de Janeiro, Rio de Janeiro, RJ 20550-900, Brazil
| | - Haroldo Moraes
- Department of Ophthalmology, Hospital Universitário Da Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-590, Brazil
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Alves BM, Siqueira JD, Prellwitz IM, Botelho OM, Da Hora VP, Sanabani S, Recordon-Pinson P, Fleury H, Soares EA, Soares MA. Estimating HIV-1 Genetic Diversity in Brazil Through Next-Generation Sequencing. Front Microbiol 2019; 10:749. [PMID: 31024510 PMCID: PMC6465556 DOI: 10.3389/fmicb.2019.00749] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/25/2019] [Indexed: 12/26/2022] Open
Abstract
Approximately 36.7 million people were living with the human immunodeficiency virus (HIV) at the end of 2016 according to UNAIDS, representing a global prevalence rate of 0.8%. In Brazil, an HIV prevalence of 0.24% has been estimated, which represents approximately 830,000 individuals living with the virus. As a touristic and commercial hub in Latin America, Brazil harbors an elevated HIV genetic variability, further contributed by the selective pressure exerted by the host immune system and by antiretroviral treatment. Through the progress of the next-generation sequencing (NGS) techniques, it has been possible to expand the study of HIV genetic diversity, evolutionary, and epidemic processes, allowing the generation of HIV complete or near full-length genomes (NFLG) and improving the characterization of intra- and interhost diversity of viral populations. Greater sensitivity in the detection of viral recombinant forms represents one of the major improvements associated with this development. It is possible to identify unique or circulating recombinant forms using the near full-length viral genomes with increasing accuracy. It also permits the characterization of multiple viral infections within individual hosts. Previous Brazilian studies using NGS to analyze HIV diversity were able to identify several distinct unique and circulating recombinant forms and evidenced dual infections. These data unveiled unprecedented high rates of viral recombination and highlighted that novel recombinants are continually arising in the Brazilian epidemic. In the pooled analysis depicted in this report, HIV subtypes have been determined from HIV-positive patients in five states of Brazil with some of the highest HIV prevalence, three in the Southeast (Rio de Janeiro, São Paulo, and Minas Gerais), one in the Northeast (Pernambuco) and one in the South (Rio Grande do Sul). Combined data analysis showed a significant prevalence of recombinant forms (29%; 101/350), and a similar 26% when only NFLGs were considered. Moreover, the analysis was able to evidence the occurrence of multiple infections in some individuals. Our data highlight the great HIV genetic diversity found in Brazil and unveils a more accurate scenario of the HIV evolutionary dynamics in the region.
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Affiliation(s)
- Brunna M Alves
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Juliana D Siqueira
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Isabel M Prellwitz
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Ornella M Botelho
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Vanusa P Da Hora
- Laboratório de Biologia Molecular, Escola de Medicina, Universidade Federal do Rio Grande, Rio Grande do Sul, Brazil
| | - Sabri Sanabani
- LIM-3, Hospital das Clinicas FMUSP, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | | | - Hervé Fleury
- CNRS MFP-UMR 5234, University Hospital of Bordeaux, University of Bordeaux, Bordeaux, France
| | - Esmeralda A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Marcelo A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.,Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Pimenta ATM, Correa IA, Melli PPDS, Abduch R, Duarte G, Couto-Fernandez JC, Quintana SM. HIV-1 genetic diversity and resistance to antiretroviral drugs among pregnant women in Ribeirão Preto (SP), Brazil. Cross-sectional study. SAO PAULO MED J 2018; 136:129-135. [PMID: 29791608 PMCID: PMC9879551 DOI: 10.1590/1516-3180.2017.0233011017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 10/01/2017] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Increasing genetic diversity of HIV-1 and emergence of drug-resistant mutations may reduce the efficacy of antiretroviral therapy and prophylaxis that are used to prevent mother-to-child transmission. The aim of this study was to assess the genetic diversity and prevalence of drug-resistant mutations among HIV-infected pregnant women. DESIGN AND SETTING Cross-sectional study at an outpatient clinic for infectious diseases within gynecology and obstetrics. METHODS This study evaluated the dynamics of HIV-1 subtypes and the prevalence of transmitted and acquired drug-resistant mutations among 38 HIV-infected pregnant women (20 previously exposed to antiretroviral therapy and 18 naive), in Ribeirão Preto (SP), Brazil, between 2010 and 2011. Genotyping was performed by means of molecular sequencing of the protease and reverse transcriptase regions of the HIV-1 pol gene. RESULTS Subtype B was identified in 84.2% of the samples, recombinant forms between B and F in 7.9%, subtype F1 in 5.3% and the recombinant form K/F in 2.6%. No mutation associated with transmitted drug resistance was detected in the samples from the naive pregnant women, whereas mutations associated with acquired drug resistance were found in 35.0% of the pregnant women previously exposed to antiretroviral therapy. CONCLUSION The results showed that subtype B predominated, while there was low prevalence of sequences with transmitted drug resistance.
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Affiliation(s)
- Ana Teresa Mancini Pimenta
- MSc, PhD. Biologist, Department of Gynecology and Obstetrics, Faculdade de Medicina de Ribeirão Preto (FMRP), Universidade de São Paulo (USP), Ribeirão Preto (SP), Brazil
| | | | - Patricia Pereira dos Santos Melli
- MD, PhD. Attending Physician, Department of Obstetrics and Gynecology, University Hospital, Faculdade de Medicina de Ribeirão Preto (FMRP), Universidade de São Paulo (USP), Ribeirão Preto (SP), Brazil
| | - Renata Abduch
- MD. Physician, Department of Obstetrics and Gynecology, Faculdade de Medicina de Ribeirão Preto (FMRP), Universidade de São Paulo (USP), Ribeirão Preto (SP), Brazil
| | - Geraldo Duarte
- MD, PhD. Professor, Department of Obstetrics and Gynecology, Faculdade de Medicina de Ribeirão Preto (FMRP), Universidade de São Paulo (USP), Ribeirão Preto (SP), Brazil
| | - José Carlos Couto-Fernandez
- MSc, PhD. Researcher, Laboratory of AIDS and Molecular Immunology, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro (RJ), Brazil
| | - Silvana Maria Quintana
- MD, PhD. Associate Professor, Department of Obstetrics and Gynecology, Faculdade de Medicina de Ribeirão Preto (FMRP), Universidade de São Paulo (USP), Ribeirão Preto (SP), Brazil
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Contribution of Epidemiological Predictors in Unraveling the Phylogeographic History of HIV-1 Subtype C in Brazil. J Virol 2015; 89:12341-8. [PMID: 26423943 DOI: 10.1128/jvi.01681-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/22/2015] [Indexed: 12/24/2022] Open
Abstract
UNLABELLED The phylogeographic history of the Brazilian HIV-1 subtype C (HIV-1C) epidemic is still unclear. Previous studies have mainly focused on the capital cities of Brazilian federal states, and the fact that HIV-1C infections increase at a higher rate than subtype B infections in Brazil calls for a better understanding of the process of spatial spread. A comprehensive sequence data set sampled across 22 Brazilian locations was assembled and analyzed. A Bayesian phylogeographic generalized linear model approach was used to reconstruct the spatiotemporal history of HIV-1C in Brazil, considering several potential explanatory predictors of the viral diffusion process. Analyses were performed on several subsampled data sets in order to mitigate potential sample biases. We reveal a central role for the city of Porto Alegre, the capital of the southernmost state, in the Brazilian HIV-1C epidemic (HIV-1C_BR), and the northward expansion of HIV-1C_BR could be linked to source populations with higher HIV-1 burdens and larger proportions of HIV-1C infections. The results presented here bring new insights to the continuing discussion about the HIV-1C epidemic in Brazil and raise an alternative hypothesis for its spatiotemporal history. The current work also highlights how sampling bias can confound phylogeographic analyses and demonstrates the importance of incorporating external information to protect against this. IMPORTANCE Subtype C is responsible for the largest HIV infection burden worldwide, but our understanding of its transmission dynamics remains incomplete. Brazil witnessed a relatively recent introduction of HIV-1C compared to HIV-1B, but it swiftly spread throughout the south, where it now circulates as the dominant variant. The northward spread has been comparatively slow, and HIV-1B still prevails in that region. While epidemiological data and viral genetic analyses have both independently shed light on the dynamics of spread in isolation, their combination has not yet been explored. Here, we complement publically available sequences and new genetic data from 13 cities with epidemiological data to reconstruct the history of HIV-1C spread in Brazil. The combined approach results in more robust reconstructions and can protect against sampling bias. We found evidence for an alternative view of the HIV-1C spatiotemporal history in Brazil that, contrary to previous explanations, integrates seamlessly with other observational data.
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Boyapalle S, Xu W, Raulji P, Mohapatra S, Mohapatra SS. A Multiple siRNA-Based Anti-HIV/SHIV Microbicide Shows Protection in Both In Vitro and In Vivo Models. PLoS One 2015; 10:e0135288. [PMID: 26407080 PMCID: PMC4583459 DOI: 10.1371/journal.pone.0135288] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 07/20/2015] [Indexed: 12/14/2022] Open
Abstract
Human immunodeficiency virus (HIV) types 1 and 2 (HIV-1 and HIV-2) are the etiologic agents of AIDS. Most HIV-1 infected individuals worldwide are women, who acquire HIV infections during sexual contact. Blocking HIV mucosal transmission and local spread in the female lower genital tract is important in preventing infection and ultimately eliminating the pandemic. Microbicides work by destroying the microbes or preventing them from establishing an infection. Thus, a number of different types of microbicides are under investigation, however, the lack of their solubility and bioavailability, and toxicity has been major hurdles. Herein, we report the development of multifunctional chitosan-lipid nanocomplexes that can effectively deliver plasmids encoding siRNA(s) as microbicides without adverse effects and provide significant protection against HIV in both in vitro and in vivo models. Chitosan or chitosan-lipid (chlipid) was complexed with a cocktail of plasmids encoding HIV-1-specific siRNAs (psiRNAs) and evaluated for their efficacy in HEK-293 cells, PBMCs derived from nonhuman primates, 3-dimensional human vaginal ectocervical tissue (3D-VEC) model and also in non-human primate model. Moreover, prophylactic administration of the chlipid to deliver a psiRNA cocktail intravaginally with a cream formulation in a non-human primate model showed substantial reduction of SHIV (simian/human immunodeficiency virus SF162) viral titers. Taken together, these studies demonstrate the potential of chlipid-siRNA nanocomplexes as a potential genetic microbicide against HIV infections.
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Affiliation(s)
- Sandhya Boyapalle
- Department of Internal Medicine -Division of Translational Medicine and Nanomedicine Research Center, University of South Florida, Tampa, Florida, United States of America
- Transgenex Nanobiotech Inc, Tampa, Florida, United States of America
| | - Weidong Xu
- Department of Internal Medicine -Division of Translational Medicine and Nanomedicine Research Center, University of South Florida, Tampa, Florida, United States of America
- Transgenex Nanobiotech Inc, Tampa, Florida, United States of America
| | - Payal Raulji
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
- Transgenex Nanobiotech Inc, Tampa, Florida, United States of America
| | - Subhra Mohapatra
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
- James A Haley VA Hospital, Tampa, Florida, United States of America
| | - Shyam S Mohapatra
- Department of Internal Medicine -Division of Translational Medicine and Nanomedicine Research Center, University of South Florida, Tampa, Florida, United States of America
- James A Haley VA Hospital, Tampa, Florida, United States of America
- * E-mail:
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