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He Y, Tang Y, Hua Q, Li X, Ge Y, Liu Y, Tang R, Tian Y, Li W. Exploring Dynamic Changes in HIV-1 Molecular Transmission Networks and Key Influencing Factors: Cross-Sectional Study. JMIR Public Health Surveill 2024; 10:e56593. [PMID: 38810253 PMCID: PMC11170051 DOI: 10.2196/56593] [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: 01/21/2024] [Revised: 02/19/2024] [Accepted: 05/05/2024] [Indexed: 05/31/2024] Open
Abstract
BACKGROUND The HIV-1 molecular network is an innovative tool, using gene sequences to understand transmission attributes and complementing social and sexual network studies. While previous research focused on static network characteristics, recent studies' emphasis on dynamic features enhances our understanding of real-time changes, offering insights for targeted interventions and efficient allocation of public health resources. OBJECTIVE This study aims to identify the dynamic changes occurring in HIV-1 molecular transmission networks and analyze the primary influencing factors driving the dynamics of HIV-1 molecular networks. METHODS We analyzed and compared the dynamic changes in the molecular network over a specific time period between the baseline and observed end point. The primary factors influencing the dynamic changes in the HIV-1 molecular network were identified through univariate analysis and multivariate analysis. RESULTS A total of 955 HIV-1 polymerase fragments were successfully amplified from 1013 specimens; CRF01_AE and CRF07_BC were the predominant subtypes, accounting for 40.8% (n=390) and 33.6% (n=321) of the specimens, respectively. Through the analysis and comparison of the basic and terminal molecular networks, it was discovered that 144 sequences constituted static molecular networks, and 487 sequences contributed to the formation of dynamic molecular networks. The findings of the multivariate analysis indicated that the factors occupation as a student, floating population, Han ethnicity, engagement in occasional or multiple sexual partnerships, participation in anal sex, and being single were independent risk factors for the dynamic changes observed in the HIV-1 molecular network, and the odds ratio (OR; 95% CIs) values were 2.63 (1.54-4.47), 1.83 (1.17-2.84), 2.91 (1.09-7.79), 1.75 (1.06-2.90), 4.12 (2.48-6.87), 5.58 (2.43-12.80), and 2.10 (1.25-3.54), respectively. Heterosexuality and homosexuality seem to exhibit protective effects when compared to bisexuality, with OR values of 0.12 (95% CI 0.05-0.32) and 0.26 (95% CI 0.11-0.64), respectively. Additionally, the National Eight-Item score and sex education experience were also identified as protective factors against dynamic changes in the HIV-1 molecular network, with OR values of 0.12 (95% CI 0.05-0.32) and 0.26 (95% CI 0.11-0.64), respectively. CONCLUSIONS The HIV-1 molecular network analysis showed 144 sequences in static networks and 487 in dynamic networks. Multivariate analysis revealed that occupation as a student, floating population, Han ethnicity, and risky sexual behavior were independent risk factors for dynamic changes, while heterosexuality and homosexuality were protective compared to bisexuality. A higher National Eight-Item score and sex education experience were also protective factors. The identification of HIV dynamic molecular networks has provided valuable insights into the characteristics of individuals undergoing dynamic alterations. These findings contribute to a better understanding of HIV-1 transmission dynamics and could inform targeted prevention strategies.
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Affiliation(s)
- Yan He
- Department of Infection Management, Nanjing Drum Tower Hospital, Nanjing, China
| | - Ying Tang
- Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Qun Hua
- Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Xin Li
- Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - You Ge
- School of Public Health, Southeast University, Nanjing, China
| | - Yangyang Liu
- School of Public Health, Southeast University, Nanjing, China
| | - Rong Tang
- Nanjing Qixia District Center for Disease Control and Prevention, Nanjing, China
| | - Ye Tian
- Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Li
- Children's Hospital of Nanjing Medical University, Nanjing, China
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Cesar GA, do Lago BV, Ortiz Tanaka TS, Zanini PB, Bandeira LM, Puga MAM, Pires Fernandes FR, Pinto CS, Castro LS, Bertolacci-Rocha LG, dos Santos Fernandes CE, de Rezende GR, Motta-Castro ARC. Differences in risky sexual behaviors and HIV prevalence between men who have sex with men and transgender women in the Midwest Brazil. PLOS GLOBAL PUBLIC HEALTH 2024; 4:e0003061. [PMID: 38709753 PMCID: PMC11073717 DOI: 10.1371/journal.pgph.0003061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 03/05/2024] [Indexed: 05/08/2024]
Abstract
Men who have sex with men (MSM) and transgender women (TW) are disproportionally affected by HIV infection. This cross-sectional study evaluated the HIV-1/2 prevalence, risk factors and HIV molecular features of MSM and TW from Midwest Brazil. Four hundred and thirty participants (278 MSM and 152 TW) from Mato Grosso do Sul, Brazil, were interviewed and tested for HIV-1/2 infection between November 2011 and September 2013. Participants who were assigned male at birth, older than 18 years old and self-declared as MSM or TW were recruited from LGBT+ associations, as well as public (parks, square, streets, etc) and private [nightclubs, saunas, brothels, etc] places. The prevalence of HIV-1 was 14.4% (9.0% among MSM and 24% among TW; p<0.001). The factor independently associated with HIV-1 infection among MSM was being 30 years-old or older. Among TW, having suffered sexual coercion, lifetime syphilis infection and hepatitis C virus exposure were associated with HIV-1 infection. Phylogenetic analyses classified 65% sequences as subtype B and 35% as possible recombinants. All but one recombinant sample were from TW individuals. High HIV-1 prevalences were observed in both groups, highlighting the urgent need to devise specific HIV interventions targeting these key populations. Notably, TWs are more vulnerable to HIV infection, which was associated with sexual violence and co-infection with other STIs. With regard to MSM, being 30 years old or older was significanty associated to HIV, reinforcing the idea that MSM are less exposed [or exposed later] to STIs than TWs, although MSM are clearly more vulnerable than the general population.
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Affiliation(s)
- Gabriela Alves Cesar
- Laboratory of Clinical Immunology, Federal University of Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Bárbara Vieira do Lago
- Laboratory of Viral Hepatitis, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- Institute of Immunobiological Technology (Bio-Manguinhos), Fiocruz, Rio de Janeiro, Brazil
| | - Tayana Serpa Ortiz Tanaka
- Laboratory of Clinical Immunology, Federal University of Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Priscila Brunini Zanini
- Laboratory of Clinical Immunology, Federal University of Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Larissa Melo Bandeira
- Laboratory of Clinical Immunology, Federal University of Mato Grosso do Sul, Campo Grande, MS, Brazil
| | | | | | - Clarice Souza Pinto
- Secretary of Health of the State of Mato Grosso do Sul, Campo Grande, MS, Brazil
| | | | | | | | | | - Ana Rita Coimbra Motta-Castro
- Laboratory of Clinical Immunology, Federal University of Mato Grosso do Sul, Campo Grande, MS, Brazil
- Laboratory of Molecular Virology, Oswaldo Cruz Foundation, Mato Grosso do Sul, Campo Grande, MS, Brazil
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Srivastva S, Chakravarty J, Kushwaha AK. Prevalence of HIV Drug Resistance Mutations among Treatment-Naive People Living with HIV in a Tertiary Care Center in India. Am J Trop Med Hyg 2024; 110:713-718. [PMID: 38442417 PMCID: PMC10993842 DOI: 10.4269/ajtmh.23-0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 11/28/2023] [Indexed: 03/07/2024] Open
Abstract
India has the third-largest number of people living with HIV (PLHIV) in the world. A national program provides free access to standard uniform antiretroviral therapy. However, the program is not monitored by comprehensive drug resistance surveys. The aim of this study was to determine the prevalence of HIV drug resistance mutations (DRMs) among treatment-naive PLHIV in a large antiretroviral treatment center of the national program. This cross-sectional study was done in 2017 and involved 200 consecutive treatment-naive PLHIV. A target fragment of 1,306 bp in the reverse transcriptase and protease regions was amplified. Identification of mutations and drug resistance interpretation was done by HIV Genotypic Resistance Interpretation and International Antiviral Society-USA list. Sequencing was successful in 177 samples. The majority (98.8%; 175/177) belonged to subtype C. Nineteen of 177 patients (10.7%; 95% CI: 6.2%-15.3%) had at least one major DRM. The prevalence of non-nucleoside reverse transcriptase inhibitor (NNRTI) mutations was 10.2% (18/177). The most frequent mutations were E138A/K, A98G, K103N, V179D, and K101H/E. The prevalence of nucleoside reverse transcriptase inhibitor (NRTI) mutations was 1.1% (2/177). None of the samples had major protease inhibitor resistance mutations. The prevalence of NNRTI mutations in this study was >10%, crossing the threshold recommended by the WHO to change the NNRTI-based first-line regimen to non-NNRTI based. In 2021, the national program replaced efavirenz with dolutegravir in the first-line regimen of tenofovir, lamivudine, and efavirenz. As the majority (64%) of PLHIV in India are accessing free ART from the national program, this study highlights the need for regular nationally representative drug resistance surveys for optimizing antiretroviral regimens in the program.
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Affiliation(s)
- Shweta Srivastva
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Jaya Chakravarty
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Anurag Kumar Kushwaha
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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Schnaufer EC, Barbosa MS, Marques MF, Brito GT, Ferreira TS, Ribeiro AD, Valiente AC, Machado IR, Gonçalves CC, Tanaka TS, Guimarães ML, Ribeiro SM, Croda J, Simionatto S. Prevalence of HIV-1 infection and associated characteristics in a Brazilian indigenous population: a cross-sectional study. LANCET REGIONAL HEALTH. AMERICAS 2023; 25:100562. [PMID: 37559945 PMCID: PMC10407292 DOI: 10.1016/j.lana.2023.100562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 06/29/2023] [Accepted: 07/10/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND Despite significant progress in the areas of prevention, diagnosis, and treatment, HIV continues to result in a substantial number of fatalities on a global scale each year. Gaining insights from epidemiological data can prove instrumental in the development of health promotion strategies, particularly within vulnerable populations, such as indigenous groups. Consequently, our study aimed to investigate the prevalence of HIV infection within the indigenous population residing in the second-largest region of Brazil. Additionally, we sought to explore the subtypes of HIV-1 and detect any drug-resistance mutations present within this population. METHODS In this cross-sectional study, we aimed to evaluate the prevalence of HIV-1 infection and explore its associated characteristics within the indigenous population residing in the villages of Jaguapiru and Bororó, located in the Dourados area of Mato Grosso do Sul (MS), Brazil. Blood samples were collected for rapid HIV screening, serological tests, nucleic acid amplification, and HIV subtyping. Additionally, the HIV-1 viral load and CD4+ T lymphocyte count of the people living with HIV (PLHIV) were assessed at the time of recruitment and 24 weeks later. FINDINGS Out of the 2190 invited individuals, 1927 (88%) were included in this study. The average age of the participants was 34.2 (±13.8) years, with a majority of 74% being female. Moreover, 68.44% of the participants identified themselves as belonging to the Guarani-Kaiowa ethnic group. HIV seroprevalence was 0.93% (18/1927), and 73.22% (1411/1927) were unaware of their serological status. The prevalence of HIV-1 was higher in single indigenous people [10/617 (1.62%)], who received government benefits [14/1021 (1.37%)], had less than five years of formal education [11/685 (1.61%)], had sexual intercourse with users of injectable drugs [2/21 (9.52%)], with history of sexually transmitted infections (STIs) [10/62 (16.2%)] and incarceration [3/62 (4.84%)]. Of 18 positive samples, 44.4% (8/18) were successfully amplified, and HIV-1 subtype C was prevalent. Furthermore, we identified HIV-1 drug resistance mutations in four patients, specifically from the classes of Protease Inhibitor, Nucleoside Reverse Transcriptase Inhibitor, and Non-Nucleoside Reverse Transcriptase Inhibitor. Notably, three of these patients exhibited a high viral load even after 24 weeks of undergoing antiretroviral therapy. Out of the 18 PLHIV, 66.66% (12/18) had a viral load below 1000 copies/mL, while 50% (9/18) had a CD4+ T lymphocytes count greater than 350 cells/mL after 24 weeks of treatment. INTERPRETATION Despite the concerted efforts to control HIV infection, the prevalence observed in the indigenous population under study surpassed that reported in other Brazilian indigenous groups. This disparity highlights the disproportionate impact of the disease on this particular group. The detection of drug-resistance mutations further emphasizes the critical need to expand diagnostic coverage, closely monitor treatment strategies, and maintain ongoing molecular surveillance. These measures are imperative for enhancing HIV management within this vulnerable population. FUNDING This study was partially funded by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Fundação de Apoio ao Desenvolvimento do Ensino, Ciência e Tecnologia do Estado de Mato Grosso do Sul (FUNDECT), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Secretaria do Estado de Saúde (SES) of Governo do Estado de Mato Grosso do Sul, and Universidade Federal da Grande Dourados (UFGD).
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Affiliation(s)
- Erica C.S. Schnaufer
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados (UFGD), Dourados, Mato Grosso do Sul, Brazil
| | - Marcelo S. Barbosa
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados (UFGD), Dourados, Mato Grosso do Sul, Brazil
| | - Michele F.R. Marques
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados (UFGD), Dourados, Mato Grosso do Sul, Brazil
| | - Gabriel T. Brito
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados (UFGD), Dourados, Mato Grosso do Sul, Brazil
| | - Tiago S. Ferreira
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados (UFGD), Dourados, Mato Grosso do Sul, Brazil
| | - Anny D.C. Ribeiro
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados (UFGD), Dourados, Mato Grosso do Sul, Brazil
| | - Anna C. Valiente
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados (UFGD), Dourados, Mato Grosso do Sul, Brazil
| | - Indianara R. Machado
- Distrito Sanitário Especial Indígena (DSEI), Dourados, Mato Grosso do Sul, Brazil
- Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Crhistinne C.M. Gonçalves
- Universidade Federal do Mato Grosso do Sul (UFMS), Campo Grande, Mato Grosso do Sul, Brazil
- Secretaria Estadual de Saúde (SES), Campo Grande, Mato Grosso do Sul, Brazil
| | - Tayana S.O. Tanaka
- Universidade Federal do Mato Grosso do Sul (UFMS), Campo Grande, Mato Grosso do Sul, Brazil
| | - Monick L. Guimarães
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Suzana M. Ribeiro
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados (UFGD), Dourados, Mato Grosso do Sul, Brazil
| | - Julio Croda
- Fundação Oswaldo Cruz (FIOCRUZ), Campo Grande, Mato Grosso do Sul, Brazil
- Faculdade de Medicina (FAMED), Universidade Federal do Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Simone Simionatto
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados (UFGD), Dourados, Mato Grosso do Sul, Brazil
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Yan J, Zhang W, Luo H, Wang X, Ruan L. Development and validation of a scoring system for the prediction of HIV drug resistance in Hubei province, China. Front Cell Infect Microbiol 2023; 13:1147477. [PMID: 37234779 PMCID: PMC10208424 DOI: 10.3389/fcimb.2023.1147477] [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: 01/18/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Objective The present study aimed to build and validate a new nomogram-based scoring system for the prediction of HIV drug resistance (HIVDR). Design and methods Totally 618 patients with HIV/AIDS were included. The predictive model was created using a retrospective set (N = 427) and internally validated with the remaining cases (N = 191). Multivariable logistic regression analysis was carried out to fit a model using candidate variables selected by Least absolute shrinkage and selection operator (LASSO) regression. The predictive model was first presented as a nomogram, then transformed into a simple and convenient scoring system and tested in the internal validation set. Results The developed scoring system consisted of age (2 points), duration of ART (5 points), treatment adherence (4 points), CD4 T cells (1 point) and HIV viral load (1 point). With a cutoff value of 7.5 points, the AUC, sensitivity, specificity, PLR and NLR values were 0.812, 82.13%, 64.55%, 2.32 and 0.28, respectively, in the training set. The novel scoring system exhibited a favorable diagnostic performance in both the training and validation sets. Conclusion The novel scoring system can be used for individualized prediction of HIVDR patients. It has satisfactory accuracy and good calibration, which is beneficial for clinical practice.
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Affiliation(s)
- Jisong Yan
- Department of Respiratory and Critical Care Medicine, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical Sciences, Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology and Wuhan Jinyintan Hospital, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Wenyuan Zhang
- Department of Infectious Diseases, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical Sciences, Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology and Wuhan Jinyintan Hospital, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Hong Luo
- Department of Respiratory and Critical Care Medicine, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical Sciences, Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology and Wuhan Jinyintan Hospital, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xianguang Wang
- Department of Respiratory and Critical Care Medicine, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical Sciences, Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology and Wuhan Jinyintan Hospital, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Lianguo Ruan
- Department of Infectious Diseases, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical Sciences, Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology and Wuhan Jinyintan Hospital, Chinese Academy of Sciences, Wuhan, Hubei, China
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Characterization of HIV-1 Transmission Clusters Inferred from the Brazilian Nationwide Genotyping Service Database. Viruses 2022; 14:v14122768. [PMID: 36560771 PMCID: PMC9783618 DOI: 10.3390/v14122768] [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: 10/05/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
The study of HIV-1 transmission networks inferred from viral genetic data can be used to clarify important factors about the dynamics of HIV-1 transmission, such as network growth rate and demographic composition. In Brazil, HIV transmission has been stable since the early 2000s and the study of transmission clusters can provide valuable data to understand the drivers of virus spread. In this work, we analyzed a nation-wide database of approximately 53,000 HIV-1 nucleotide pol sequences sampled from genotyped patients from 2008-2017. Phylogenetic trees were reconstructed for the HIV-1 subtypes B, C and F1 in Brazil and transmission clusters were inferred by applying genetic distances thresholds of 1.5%, 3.0% and 4.5%, as well as high (>0.9) cluster statistical support. An odds ratio test revealed that young men (15-24 years) and individuals with more years of education presented higher odds to cluster. The assortativity coefficient revealed that individuals with similar demographic features tended to cluster together, with emphasis on features, such as place of residence and age. We also observed that assortativity weakens as the genetic distance threshold increases. Our results indicate that the phylogenetic clusters identified here are likely representative of the contact networks that shape HIV transmission, and this is a valuable tool even in sites with low sampling density, such as Brazil.
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Molecular Epidemiology of HIV-1 among Prisoners in Central Brazil and Evidence of Transmission Clusters. Viruses 2022; 14:v14081660. [PMID: 36016283 PMCID: PMC9415882 DOI: 10.3390/v14081660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 02/04/2023] Open
Abstract
Higher rates of human immunodeficiency virus (HIV) infection have been detected in prisoners when compared with the general population, but research into HIV molecular epidemiology and its transmission network has been lacking among them. Thus, this study aimed to verify potential HIV molecular transmission networks among prisoners. In addition, we aimed to describe the mutations related to antiretroviral resistance in these isolates. Thus, we conducted a cross-sectional survey from 2013 to 2018 in prisons in Central-Western Brazil, and the final sampling composed of 84 prisoners. Proviral DNA was extracted from each whole blood sample followed by amplification of the partial polymerase gene and sequencing. Forty-nine sequences (58.3%) were classified as subtype B, followed by C (14.3%), D, and F1 (2.4% each). A complex and dynamic HIV-1 epidemic is observed in the prisons, as 25% of the sequences were recombinant forms. We detected 15 HIV transmission clusters composed of at least two sequences, that included not only prisoners but also individuals from the general population from the same State with a variety of risk behaviors. Thirty-two percent (32.0%) of treatment-experienced prisoners had at least one drug resistance mutation (DRM), while transmitted DRMs were found in 5.9% of the prisoners. We highlight the urgent need for routine surveillance of HIV-1 infection including resistance genotypic tests considering the high disease burden, risky behaviors inside prisons, and the dynamic relationship of prisoners with the outside community.
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Zhao H, Lu Z, Lu Y. The potential of probiotics in the amelioration of hyperuricemia. Food Funct 2022; 13:2394-2414. [PMID: 35156670 DOI: 10.1039/d1fo03206b] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hyperuricemia is a common disease caused by metabolic disorders or the excessive intake of high-purine foods. Persistent hyperuricemia in extreme cases induces gout, and asymptomatic hyperuricemia is probably linked to other metabolic diseases, such as hypertension. The typical damage caused by asymptomatic hyperuricemia includes inflammation, oxidative stress and gut dysbiosis. Probiotics have broad potential applications as food additives, not as drug therapies, in the amelioration of hyperuricemia. In this review, we describe novel methods for potential hyperuricemia amelioration with probiotics. The pathways through which probiotics may ameliorate hyperuricemia are discussed, including the decrease in uric acid production through purine assimilation and XOD (xanthine oxidase) inhibition as well as enhanced excretion of uric acid production by promoting ABCG2 (ATP binding cassette subfamily G member 2) activity, respectively. Three possible probiotic-related therapeutic pathways for alleviating the syndrome of hyperuricemia are also summarized. The first mechanism is to alleviate the oxidation and inflammation induced by hyperuricemia through the inhibition of NLRP3 inflammasome, the second is to restore damaged intestinal epithelium barriers and prevent gut microbiota dysbiosis, and the third is to enhance the innate immune system by increasing the secretion of immunoglobulin A (sIgA) to resist the stimulus by hyperuricemia. We propose that future research should focus on superior strain resource isolation and insight into the cause-effect mechanisms of probiotics for hyperuricemia amelioration. The safety and effects of the application of probiotics in clinical use also need verification.
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Affiliation(s)
- Hongyuan Zhao
- College of Food Science & Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zhaoxin Lu
- College of Food Science & Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yingjian Lu
- College of Food Science & Engineering, Nanjing University of Finance and Economics, Nanjing 210023, China.
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Cappelle J, Furey N, Hoem T, Ou TP, Lim T, Hul V, Heng O, Chevalier V, Dussart P, Duong V. Longitudinal monitoring in Cambodia suggests higher circulation of alpha and betacoronaviruses in juvenile and immature bats of three species. Sci Rep 2021; 11:24145. [PMID: 34921180 PMCID: PMC8683416 DOI: 10.1038/s41598-021-03169-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 11/25/2021] [Indexed: 12/28/2022] Open
Abstract
Recent studies suggest that coronaviruses circulate widely in Southeast Asian bat species and that the progenitors of the SARS-Cov-2 virus could have originated in rhinolophid bats in the region. Our objective was to assess the diversity and circulation patterns of coronavirus in several bat species in Southeast Asia. We undertook monthly live-capture sessions and sampling in Cambodia over 17 months to cover all phases of the annual reproduction cycle of bats and test specifically the association between their age and CoV infection status. We additionally examined current information on the reproductive phenology of Rhinolophus and other bat species presently known to occur in mainland southeast China, Vietnam, Laos and Cambodia. Results from our longitudinal monitoring (573 bats belonging to 8 species) showed an overall proportion of positive PCR tests for CoV of 4.2% (24/573) in cave-dwelling bats from Kampot and 4.75% (22/463) in flying-foxes from Kandal. Phylogenetic analysis showed that the PCR amplicon sequences of CoVs (n = 46) obtained clustered in Alphacoronavirus and Betacoronavirus. Interestingly, Hipposideros larvatus sensu lato harbored viruses from both genera. Our results suggest an association between positive detections of coronaviruses and juvenile and immature bats in Cambodia (OR = 3.24 [1.46-7.76], p = 0.005). Since the limited data presently available from literature review indicates that reproduction is largely synchronized among rhinolophid and hipposiderid bats in our study region, particularly in its more seasonal portions (above 16° N), this may lead to seasonal patterns in CoV circulation. Overall, our study suggests that surveillance of CoV in insectivorous bat species in Southeast Asia, including SARS-CoV-related coronaviruses in rhinolophid bats, could be targeted from June to October for species exhibiting high proportions of juveniles and immatures during these months. It also highlights the need to develop long-term longitudinal surveys of bats and improve our understanding of their ecology in the region, for both biodiversity conservation and public health reasons.
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Affiliation(s)
- Julien Cappelle
- CIRAD, UMR ASTRE (Animal, Santé, Territoires, Risques, Ecosystèmes), TA A 117/E, Campus International de Baillarguet, 34398, Montpellier CEDEX 5, France.
- ASTRE, CIRAD, INRAE, Univ Montpellier, Montpellier, France.
| | - Neil Furey
- Harrison Institute, Sevenoaks, Kent, England
- Fauna and Flora International, Phnom Penh, Cambodia
| | - Thavry Hoem
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Tey Putita Ou
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Thona Lim
- Free the Bears, Phnom Penh, Cambodia
| | - Vibol Hul
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Oudam Heng
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Véronique Chevalier
- CIRAD, UMR ASTRE (Animal, Santé, Territoires, Risques, Ecosystèmes), TA A 117/E, Campus International de Baillarguet, 34398, Montpellier CEDEX 5, France
- ASTRE, CIRAD, INRAE, Univ Montpellier, Montpellier, France
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
- Virology Unit, Institut Pasteur de Madagascar, Institut Pasteur International Network, Antananarivo, Madagascar
| | - Veasna Duong
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
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10
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Gräf T, Bello G, Andrade P, Arantes I, Pereira JM, da Silva ABP, Veiga RV, Mariani D, Boullosa LT, Arruda MB, Fernandez JCC, Dennis AM, Rasmussen DA, Tanuri A. HIV-1 molecular diversity in Brazil unveiled by 10 years of sampling by the national genotyping network. Sci Rep 2021; 11:15842. [PMID: 34349153 PMCID: PMC8338987 DOI: 10.1038/s41598-021-94542-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/12/2021] [Indexed: 12/04/2022] Open
Abstract
HIV-1 has diversified into several subtypes and recombinant forms that are heterogeneously spread around the world. Understanding the distribution of viral variants and their temporal dynamics can help to design vaccines and monitor changes in viral transmission patterns. Brazil has one of the largest HIV-1 epidemics in the western-world and the molecular features of the virus circulating in the country are still not completely known. Over 50,000 partial HIV-1 genomes sampled between 2008 and 2017 by the Brazilian genotyping network (RENAGENO) were analyzed. Sequences were filtered by quality, duplicate sequences per patient were removed and subtyping was performed with online tools and molecular phylogeny. Association between patients’ demographic data and subtypes were performed by calculating the relative risk in a multinomial analysis and trends in subtype prevalence were tested by Pearson correlation. HIV-1B was found to be the most prevalent subtype throughout the country except in the south, where HIV-1C prevails. An increasing trend in the proportion of HIV-1C and F1 was observed in several regions of the country, while HIV-1B tended to decrease. Men and highly educated individuals were more frequently infected by HIV-1B and non-B variants were more prevalent among women with lower education. Our results suggest that socio-demographic factors partially segregate HIV-1 diversity in Brazil while shaping viral transmission networks. Historical events could explain a preferential circulation of HIV-1B among men who have sex with men (MSM) and non-B variants among heterosexual individuals. In view of an increasing male/female ratio of AIDS cases in Brazil in the last 10–15 years, the decrease of HIV-1B prevalence is surprising and suggests a greater penetrance of non-B subtypes in MSM transmission chains.
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Affiliation(s)
- Tiago Gräf
- Fundação Oswaldo Cruz, Instituto Gonçalo Moniz, Rua Waldemar Falcão, 121, Salvador, 40296-710, Brazil.
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Paula Andrade
- Laboratório de AIDS e Imunologia Molecular, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ighor Arantes
- Laboratório de AIDS e Imunologia Molecular, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - João Marcos Pereira
- Laboratório de Virologia Molecular, Departamento de Genética-IB, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Laboratório de Bioinformática and Evolução Molecular, Departamento de Genética-IB, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre Bonfim Pinheiro da Silva
- Laboratório de Virologia Molecular, Departamento de Genética-IB, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Laboratório de Bioinformática and Evolução Molecular, Departamento de Genética-IB, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafael V Veiga
- Center of Data and Knowledge Integration for Health (CIDACS), Fundação Oswaldo Cruz, Instituto Gonçalo Moniz, Salvador, Brazil.,Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil
| | - Diana Mariani
- Laboratório de Virologia Molecular, Departamento de Genética-IB, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lídia Theodoro Boullosa
- Laboratório de Virologia Molecular, Departamento de Genética-IB, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mônica B Arruda
- Laboratório de Virologia Molecular, Departamento de Genética-IB, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - José Carlos Couto Fernandez
- Laboratório de AIDS e Imunologia Molecular, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ann M Dennis
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - David A Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, USA
| | - Amilcar Tanuri
- Laboratório de Virologia Molecular, Departamento de Genética-IB, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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11
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Nationwide Study of Drug Resistance Mutations in HIV-1 Infected Individuals under Antiretroviral Therapy in Brazil. Int J Mol Sci 2021; 22:ijms22105304. [PMID: 34069929 PMCID: PMC8157590 DOI: 10.3390/ijms22105304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/02/2022] Open
Abstract
The success of antiretroviral treatment (ART) is threatened by the emergence of drug resistance mutations (DRM). Since Brazil presents the largest number of people living with HIV (PLWH) in South America we aimed at understanding the dynamics of DRM in this country. We analyzed a total of 20,226 HIV-1 sequences collected from PLWH undergoing ART between 2008–2017. Results show a mild decline of DRM over the years but an increase of the K65R reverse transcriptase mutation from 2.23% to 12.11%. This increase gradually occurred following alterations in the ART regimens replacing zidovudine (AZT) with tenofovir (TDF). PLWH harboring the K65R had significantly higher viral loads than those without this mutation (p < 0.001). Among the two most prevalent HIV-1 subtypes (B and C) there was a significant (p < 0.001) association of K65R with subtype C (11.26%) when compared with subtype B (9.27%). Nonetheless, evidence for K65R transmission in Brazil was found both for C and B subtypes. Additionally, artificial neural network-based immunoinformatic predictions suggest that K65R could enhance viral recognition by HLA-B27 that has relatively low prevalence in the Brazilian population. Overall, the results suggest that tenofovir-based regimens need to be carefully monitored particularly in settings with subtype C and specific HLA profiles.
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12
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Machado LFA, Fonseca RRDS, Queiroz MAF, Oliveira-Filho AB, Cayres-Vallinoto IMV, Vallinoto ACR, Ishak MDOG, Ishak R. The Epidemiological Impact of STIs among General and Vulnerable Populations of the Amazon Region of Brazil: 30 years of Surveillance. Viruses 2021; 13:v13050855. [PMID: 34067165 PMCID: PMC8151421 DOI: 10.3390/v13050855] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/13/2022] Open
Abstract
Sexually transmitted infections (STIs) represent a worldwide public health problem and, although many of them are curable, they continue to be neglected, especially in areas with a low human development index, such as in the northern region of Brazil. This review describes the results of 30 years of studies at the Virus Laboratory at the Federal University of Pará, including the prevalence and molecular epidemiology of HIV-1, HTLV-1/2, HPV, HBV, Treponema pallidum and Chlamydia trachomatis among urban and non-urban populations, and also in vulnerable groups in the Brazilian Amazon. Control strategies and challenges in preventing STIs are discussed considering this immense geographic region, where essential health services are unable to reach the entire population, especially the most vulnerable, such as female sex workers, people who use illicit drugs, remnants of quilombolos and indigenous communities.
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Affiliation(s)
- Luiz Fernando Almeida Machado
- Laboratório de Virologia, Instituto de Ciências Biológica, Universidade Federal do Pará, Belém 66.075-110, Brazil; (R.R.d.S.F.); (M.A.F.Q.); (I.M.V.C.-V.); (A.C.R.V.); (M.d.O.G.I.); (R.I.)
- Correspondence:
| | - Ricardo Roberto de Souza Fonseca
- Laboratório de Virologia, Instituto de Ciências Biológica, Universidade Federal do Pará, Belém 66.075-110, Brazil; (R.R.d.S.F.); (M.A.F.Q.); (I.M.V.C.-V.); (A.C.R.V.); (M.d.O.G.I.); (R.I.)
| | - Maria Alice Freitas Queiroz
- Laboratório de Virologia, Instituto de Ciências Biológica, Universidade Federal do Pará, Belém 66.075-110, Brazil; (R.R.d.S.F.); (M.A.F.Q.); (I.M.V.C.-V.); (A.C.R.V.); (M.d.O.G.I.); (R.I.)
| | - Aldemir Branco Oliveira-Filho
- Grupo de Estudo e Pesquisa em Populações Vulneráveis, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança 68.600-000, Brazil;
| | - Izaura Maria Vieira Cayres-Vallinoto
- Laboratório de Virologia, Instituto de Ciências Biológica, Universidade Federal do Pará, Belém 66.075-110, Brazil; (R.R.d.S.F.); (M.A.F.Q.); (I.M.V.C.-V.); (A.C.R.V.); (M.d.O.G.I.); (R.I.)
| | - Antonio Carlos Rosário Vallinoto
- Laboratório de Virologia, Instituto de Ciências Biológica, Universidade Federal do Pará, Belém 66.075-110, Brazil; (R.R.d.S.F.); (M.A.F.Q.); (I.M.V.C.-V.); (A.C.R.V.); (M.d.O.G.I.); (R.I.)
| | - Marluísa de Oliveira Guimarães Ishak
- Laboratório de Virologia, Instituto de Ciências Biológica, Universidade Federal do Pará, Belém 66.075-110, Brazil; (R.R.d.S.F.); (M.A.F.Q.); (I.M.V.C.-V.); (A.C.R.V.); (M.d.O.G.I.); (R.I.)
| | - Ricardo Ishak
- Laboratório de Virologia, Instituto de Ciências Biológica, Universidade Federal do Pará, Belém 66.075-110, Brazil; (R.R.d.S.F.); (M.A.F.Q.); (I.M.V.C.-V.); (A.C.R.V.); (M.d.O.G.I.); (R.I.)
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13
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Zhang D, Zheng C, Li H, Li H, Liu Y, Wang X, Jia L, Chen L, Yang Z, Gan Y, Zhong Y, Han J, Li T, Li J, Zhao J, Li L. Molecular surveillance of HIV-1 newly diagnosed infections in Shenzhen, China from 2011 to 2018. J Infect 2021; 83:76-83. [PMID: 33932447 DOI: 10.1016/j.jinf.2021.04.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 12/18/2022]
Abstract
OBJECTIVES Shenzhen is suffering severe HIV epidemic. No systematic surveillance on high risk populations, HIV genetic diversity, transmitted drug resistance (TDR) and molecular transmission clusters (MTCs) have been reported yet. In this study, we described them based on newly diagnosed HIV positive cases from 2011 to 2018 in Shenzhen city, China. METHODS Plasma samples of newly reported HIV positive cases in Shenzhen, China were collected from 2011 to 2018. The HIV pol gene was amplified and sequenced for subtyping, genetic characterization, TDR and phylogenetic analysis. Demographic and risk characteristics associated with transmitted drug resistance-associated mutations (TDRAMs) and MTCs were explored by using logistic regression analyses. RESULTS 10,378 HIV pol sequences were successfully obtained from newly diagnosed patients with available background information. The most prevalent HIV-1 subtype was CRF07_BC (40.92%). CRF07_BC, CRF55_01B and URFs increased across years. Total TDR was 6.02% during 2011 to 2018. CRF01_AE, CRF08_BC, CRF55_01B and subtype B were more likely to be associated with TDRAMs than CRF07_BC. 4460 (42.98%) patients were infected with strains included in MTCs. Patients younger than 30 and over 50 years were more likely to cluster. CONCLUSIONS The prevalence of HIV-1 drug resistance and molecular transmission clusters in Shenzhen should raise a high alert. Interventions targeting on patients with strains locating in MTCs should be considered to improve prevention effect in Shenzhen.
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Affiliation(s)
- Dong Zhang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071 China
| | - Chenli Zheng
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong 518055, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071 China
| | - Hao Li
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong 518055, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071 China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071 China
| | - Lei Jia
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071 China
| | - Lin Chen
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong 518055, China
| | - Zhengrong Yang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071 China; Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong 518055, China
| | - Yongxia Gan
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071 China; Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong 518055, China
| | - Yifan Zhong
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071 China; Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong 518055, China
| | - Jingwan Han
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071 China
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071 China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071 China.
| | - Jin Zhao
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong 518055, China.
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071 China.
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14
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Fan Q, Zhang J, Luo M, Yao J, Ge R, Yan Y, Ding X, Chen W, Pan X. Analysis of the Driving Factors of Active and Rapid Growth Clusters Among CRF07_BC-Infected Patients in a Developed Area in Eastern China. Open Forum Infect Dis 2021; 8:ofab051. [PMID: 33728360 PMCID: PMC7944347 DOI: 10.1093/ofid/ofab051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 01/29/2021] [Indexed: 11/22/2022] Open
Abstract
Background The purpose of this study was to research the molecular transmission and genetic evolutionary characteristics among CRF07_BC-infected patients in a developed area in Eastern China. Methods Plasma samples from newly diagnosed HIV-1-positive patients from 2015–2018 and basic demographic and epidemiological information were obtained. Pol sequences from CRF07_BC-infected patients were selected for phylogenetic, molecular transmission network, and Bayesian evolutionary analyses. Results Pol sequences were successfully obtained from 258 samples of CRF07_BC. Phylogenetic analysis revealed 2 distinct lineages: lineage 1 (66.3%, 171/258), primarily from men who have sex with men (MSM) and some heterosexual individuals, and lineage 2 (33.7%, 87/258), primarily from heterosexual individuals. Under an optimal genetic distance of 0.01 substitutions/site, 163 individuals (63.2%, 163/258) formed 23 groups comprising 6 clusters and 17 dyads in the networks. A distinctly large and rapidly growing cluster (C1) containing 105 individuals was identified, in which MSM with ≥4 links had quite a high transmission risk (low educational background, active sexual behavior, low sexual protection awareness, etc.). According to Bayesian analyses, most C1 clades formed from 2005 to 2009, most of which were closely geographically related to CRF07_BC epidemic strains from Anhui province. Conclusions Here, we elucidated the local transmission characteristics and epidemic pattern of HIV-1 CRF07_BC, revealing that MSM (especially with ≥4 links) may be a significant driver in the formation of active and rapid growth networks in regional CRF07_BC epidemics. Thus, unique region– and risk group–specific transmission network analysis based on a molecular approach can provide critical and insightful information for more effective intervention strategies to limit future HIV-1 transmission.
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Affiliation(s)
- Qin Fan
- Department of HIV/AIDS and STDs Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Jiafeng Zhang
- Department of HIV/AIDS and STDs Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Mingyu Luo
- Department of HIV/AIDS and STDs Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Jiaming Yao
- Department of HIV/AIDS and STDs Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Rui Ge
- Division of AIDS/TB Prevention and Control, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing, China
| | - Yong Yan
- Division of AIDS/TB Prevention and Control, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing, China
| | - Xiaobei Ding
- Department of HIV/AIDS and STDs Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Wanjun Chen
- Department of HIV/AIDS and STDs Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Xiaohong Pan
- Department of HIV/AIDS and STDs Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
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15
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Silva ÁMDCE, Reis MNDG, Marinho TA, de Freitas NR, Teles SA, de Matos MAD, Carneiro MADS, Bello G, Stefani MMA, Martins RMB. Epidemiological and Molecular Characteristics of HIV-1 Infection in a Sample of Men Who Have Sex With Men in Brazil: Phylogeography of Major Subtype B and F1 Transmission Clusters. Front Microbiol 2020; 11:589937. [PMID: 33329467 PMCID: PMC7732656 DOI: 10.3389/fmicb.2020.589937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/03/2020] [Indexed: 11/16/2022] Open
Abstract
This study describes human immunodeficiency virus 1 (HIV-1) prevalence, associated factors, viral genetic diversity, transmitted drug resistance (TDR), and acquired drug resistance mutations (DRM) among a population of 522 men who have sex with men (MSM) recruited by the respondent-driven sampling (RDS) method, in Goiânia city, the capital of the State of Goiás, Central-Western Brazil. All serum samples were tested using a four-generation enzyme-linked immunosorbent assay (ELISA), and reactive samples were confirmed by immunoblotting. Plasma RNA or proviral DNA was extracted, and partial polymerase (pol) gene including the protease/reverse transcriptase (PR/RT) region was amplified and sequenced. HIV-1 subtypes were identified by phylogenetic inference and by bootscan analysis. The time and location of the ancestral strains that originated the transmission clusters were estimated by a Bayesian phylogeographic approach. TDR and DRM were identified using the Stanford databases. Overall, HIV-1 prevalence was 17.6% (95% CI: 12.6–23.5). Self-declared black skin color, receptive anal intercourse, sex with drug user partner, and history of sexually transmitted infections were factors associated with HIV-1 infection. Of 105 HIV-1-positive samples, 78 (74.3%) were sequenced and subtyped as B (65.4%), F1 (20.5%), C (3.8%), and BF1 (10.3%). Most HIV-1 subtype B sequences (67%; 34 out of 51) branched within 12 monophyletic clusters of variable sizes, which probably arose in the State of Goiás between the 1980s and 2010s. Most subtype F1 sequences (n = 14, 88%) branched in a single monophyletic cluster that probably arose in Goiás around the late 1990s. Among 78 samples sequenced, three were from patients under antiretroviral therapy (ART); two presented DRM. Among 75 ART-naïve patients, TDR was identified in 13 (17.3%; CI 95%: 9.6–27.8). Resistance mutations to non-nucleoside reverse transcriptase inhibitors (NNRTI) predominated (14.7%), followed by nucleoside reverse transcriptase inhibitor (NRTI) mutations (5.3%) and protease inhibitor (PI) mutations (1.3%). This study shows a high prevalence of HIV-1 associated with sexual risk behaviors, high rate of TDR, and high genetic diversity driven by the local expansion of different subtype B and F1 strains. These findings can contribute to the understanding about the dissemination and epidemiological and molecular characteristics of HIV-1 among the population of MSM living away from the epicenter of epidemics in Brazil.
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Affiliation(s)
| | | | - Thaís Augusto Marinho
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Brazil
| | | | | | | | | | - Gonzalo Bello
- AIDS and Molecular Immunology Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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16
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Kiros M, Alemayehu DH, Geberekidan E, Mihret A, Maier M, Abegaz WE, Mulu A. Increased HIV-1 pretreatment drug resistance with consistent clade homogeneity among ART-naive HIV-1 infected individuals in Ethiopia. Retrovirology 2020; 17:33. [PMID: 32993693 PMCID: PMC7526103 DOI: 10.1186/s12977-020-00542-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/23/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The development of pretreatment drug resistance (PDR) is becoming an obstacle to the success of antiretroviral therapy (ART). Besides, data from developing settings including Ethiopia is still limited. Therefore, this study was aimed to assess HIV-1 genetic diversity and PDR mutations among ART-naive recently diagnosed HIV-1 infected individuals in Addis Ababa, Ethiopia. METHODS Institutional based cross-sectional study was conducted from June to December 2018 in Addis Ababa among ART-naive recently diagnosed individuals. Partial HIV-1 pol region covering the entire protease (PR) and partial reverse transcriptase (RT) regions of 51 samples were amplified and sequenced using an in-house assay. Drug resistance mutations were examined using calibrated population resistance (CPR) tool version 6.0 from the Stanford HIV drug resistance database and the International Antiviral Society-USA (IAS-USA) 2019 mutation list. RESULTS According to both algorithms used, 9.8% (5/51) of analyzed samples had at least one PDR Mutation. PDR mutations to Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) were the most frequently detected (7.8% and 9.8%, according to the CPR tool and IAS-USA algorithm, respectively). The most frequently observed NNRTIs-associated mutations common to both algorithms were K103N (2%), Y188L (2%), K101E (2%), and V106A (2%), while E138A (2%) was observed according to IAS-USA only. Y115F and M184V (mutations that confer resistance to NRTIs) dual mutations were detected according to both criteria in a single study participant (2%). PDR mutation to protease inhibitors was found to be low (only G73S; 2% according to the CPR tool). Phylogenetic analysis showed that 98% (50/51) of the study participants were infected with HIV-1C virus while one individual (2%) was infected with HIV-1A1 virus. CONCLUSIONS This study showed an increased level of PDR and persistence HIV-1C clade homogeneity after 15 years of the rollout of ART and 3 decades of HIV-1C circulation in Ethiopia, respectively. Therefore, we recommend routine baseline genotypic drug resistance testing for all newly diagnosed HIV infected patients before initiating treatment. This will aid the selection of appropriate therapy in achieving the 90% of patients having an undetectable viral load in consonance with the UN target.
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Affiliation(s)
- Mulugeta Kiros
- Department of Medical Laboratory Science, College of Medicine and Health Science, Debre Tabor University, Debre Tabor, Ethiopia.
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia.
| | | | | | - Adane Mihret
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Melanie Maier
- Institute of Virology, Leipzig University, Leipzig, Germany
| | - Woldaregay Erku Abegaz
- Department of Microbiology, Parasitology, and Immunology, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
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Lai A, Bergna A, Simonetti FR, Franzetti M, Bozzi G, Micheli V, Atzori C, Ridolfo A, Zehender G, Ciccozzi M, Galli M, Balotta C. Contribution of transgender sex workers to the complexity of the HIV-1 epidemic in the metropolitan area of Milan. Sex Transm Infect 2020; 96:451-456. [PMID: 31900319 DOI: 10.1136/sextrans-2019-054103] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 09/23/2019] [Accepted: 12/12/2019] [Indexed: 01/15/2023] Open
Abstract
OBJECTIVES Transgender people are disproportionately affected by the HIV-1 epidemic. We evaluated the origin of HIV-1 variants carried by South American transgenders living in Milan by combining accurate phylogenetic methods and epidemiological data. METHODS We collected 156 HIV-1 pol sequences obtained from transgender patients engaged in sex work (TSWs) followed between 1999 and 2015 at L. Sacco Hospital, Milan, Italy. Phylogenetic analyses were conducted by HIV-TRACE, MrBayes, MacClade and Beast programs. Reference sequences were retrieved from Los Alamos and local databases. Last negative testing or proxy data from clinical records of infected individuals were used to investigate the country of infection. RESULTS Among South American TSWs, the most represented HIV-1 subtypes were B (70.5%), F1 (12.8%) and C (4.4%). Gene flow migrations of B subtype indicated significant fluxes from TSWs to Italians (21.3%) belonging to all risk groups (26.4% to heterosexuals (HEs), 18.9% to men who have sex with men (MSM), 15.1% to injecting drug users). The largest proportion of bidirectional fluxes were observed between Italians and TSWs (24.6%). For F1 subtype, bidirectional viral fluxes involved TSWs and Italians (7.1% and 14.3%), and a similar proportion of fluxes linked TSWs and Italian HEs or MSM (both 15.8%). Significant fluxes were detected from Italians to TSWs for subtype C involving both MSM (30%) and HEs (40%). Country of HIV-1 acquisition was identified for 72 subjects; overall, the largest proportion of patients with B subtype (73.5%) acquired HIV-1 infection in South America. CONCLUSIONS Our results indicated that South American transgenders largely contribute to the heterogeneity of HIV-1 variants in our country. The high number of clusters based on all subtypes indicated numerous transmission chains in which TSWs were constantly intermixed with HEs and MSM. Our results strongly advocate interventions to facilitate prevention, diagnosis and HIV-1 care continuum among transgender people.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milano, Lombardia, Italy
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milano, Lombardia, Italy
| | | | - Marco Franzetti
- Infectious Diseases Unit, Alessandro Manzoni Hospital, Lecco, Lombardia, Italy
| | - Giorgio Bozzi
- Department of Pathophysiology and Transplantation, La Fondazione IRCCS Ca' Granda Ospedale Maggiore di Milano Policlinico, Milano, Lombardia, Italy
| | - Valeria Micheli
- Department of Clinical Microbiology Virology and Diagnosis of Bioemergency, Luigi Sacco University Hospital, Milano, Lombardia, Italy
| | - Chiara Atzori
- 1st Division of Infectious Diseases, Luigi Sacco University Hospital, Milano, Lombardia, Italy
| | - Annalisa Ridolfo
- Department of Infectious Diseases, Luigi Sacco University Hospital, Milano, Lombardia, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milano, Lombardia, Italy
| | - Massimo Ciccozzi
- Unit of Clinical Pathology and Microbiology, University Campus Bio-Medico University of Rome Faculty of Medicine and Surgery, Roma, Lazio, Italy
| | - Massimo Galli
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milano, Lombardia, Italy
| | - Claudia Balotta
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milano, Lombardia, Italy
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Benzaken AS, Pereira GFM, Costa L, Tanuri A, Santos AF, Soares MA. Antiretroviral treatment, government policy and economy of HIV/AIDS in Brazil: is it time for HIV cure in the country? AIDS Res Ther 2019; 16:19. [PMID: 31412889 PMCID: PMC6694665 DOI: 10.1186/s12981-019-0234-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 08/06/2019] [Indexed: 12/21/2022] Open
Abstract
Brazil is a low-and-middle income country (LMIC) that, despite having a large population and continental dimensions, has been able to successfully fight HIV/AIDS through a number of governmental and societal measures. These included an early response to the epidemic, the development of a universal and free public health system, incisive discussions with pharmaceutical companies to reduce antiretroviral (ARV) drug prices, investments towards the development of generic drugs and compulsory licensing of ARVs. Through such measures, Brazil is among the leading LMIC towards achieving the 90-90-90 UNAIDS goals in the years to come. In this review, we analyze Brazil’s progress throughout the HIV/AIDS epidemic to achieve state-of-the-art ARV treatment and to reduce AIDS mortality in the country. The top-quality HIV/AIDS research in Brazil towards HIV prophylactic and functional cure, the next step towards the economic sustainability of the battle against HIV, is also discussed.
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