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Apetroaei MM, Velescu BȘ, Nedea MI(I, Dinu-Pîrvu CE, Drăgănescu D, Fâcă AI, Udeanu DI, Arsene AL. The Phenomenon of Antiretroviral Drug Resistance in the Context of Human Immunodeficiency Virus Treatment: Dynamic and Ever Evolving Subject Matter. Biomedicines 2024; 12:915. [PMID: 38672269 PMCID: PMC11048092 DOI: 10.3390/biomedicines12040915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Human immunodeficiency virus (HIV) is a significant global health issue that affects a substantial number of individuals across the globe, with a total of 39 million individuals living with HIV/AIDS. ART has resulted in a reduction in HIV-related mortality. Nevertheless, the issue of medication resistance is a significant obstacle in the management of HIV/AIDS. The unique genetic composition of HIV enables it to undergo rapid mutations and adapt, leading to the emergence of drug-resistant forms. The development of drug resistance can be attributed to various circumstances, including noncompliance with treatment regimens, insufficient dosage, interactions between drugs, viral mutations, preexposure prophylactics, and transmission from mother to child. It is therefore essential to comprehend the molecular components of HIV and the mechanisms of antiretroviral medications to devise efficacious treatment options for HIV/AIDS.
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Affiliation(s)
- Miruna-Maria Apetroaei
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (M.-M.A.); (M.I.N.); (C.E.D.-P.); (D.D.); (A.I.F.); (D.I.U.); (A.L.A.)
| | - Bruno Ștefan Velescu
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (M.-M.A.); (M.I.N.); (C.E.D.-P.); (D.D.); (A.I.F.); (D.I.U.); (A.L.A.)
| | - Marina Ionela (Ilie) Nedea
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (M.-M.A.); (M.I.N.); (C.E.D.-P.); (D.D.); (A.I.F.); (D.I.U.); (A.L.A.)
| | - Cristina Elena Dinu-Pîrvu
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (M.-M.A.); (M.I.N.); (C.E.D.-P.); (D.D.); (A.I.F.); (D.I.U.); (A.L.A.)
| | - Doina Drăgănescu
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (M.-M.A.); (M.I.N.); (C.E.D.-P.); (D.D.); (A.I.F.); (D.I.U.); (A.L.A.)
| | - Anca Ionela Fâcă
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (M.-M.A.); (M.I.N.); (C.E.D.-P.); (D.D.); (A.I.F.); (D.I.U.); (A.L.A.)
- Marius Nasta Institute of Pneumophthisiology, 90 Viilor Street, 050159 Bucharest, Romania
| | - Denisa Ioana Udeanu
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (M.-M.A.); (M.I.N.); (C.E.D.-P.); (D.D.); (A.I.F.); (D.I.U.); (A.L.A.)
- Marius Nasta Institute of Pneumophthisiology, 90 Viilor Street, 050159 Bucharest, Romania
| | - Andreea Letiția Arsene
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (M.-M.A.); (M.I.N.); (C.E.D.-P.); (D.D.); (A.I.F.); (D.I.U.); (A.L.A.)
- Marius Nasta Institute of Pneumophthisiology, 90 Viilor Street, 050159 Bucharest, Romania
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HIV transmission among acutely infected participants of a Dutch cohort study 2015-2021 is not associated with large, clustered outbreaks. AIDS 2023; 37:299-303. [PMID: 36305171 PMCID: PMC9794119 DOI: 10.1097/qad.0000000000003416] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
OBJECTIVE Timely identification of acute or early HIV infection (AEHI) is important to help prevent onward transmission, and understanding the number of secondary infections resulting from individuals with AEHI is key to planning HIV prevention services and case finding. DESIGN We performed a phylogenetic investigation of a dense sample of individuals with AEHI who took part in the Netherlands Cohort Study on Acute HIV infection (NOVA) in the Netherlands during 2015-2021. METHODS Transmission clusters were identified using phylogenetic analyses based on HIV pol sequences. The Tamura-Nei model was used to estimate genetic distance. A number of 1000 bootstraps was used to check the reliability of clustering using maximum likelihood. A cluster was defined as having a bootstrap value of at least 95% and a genetic distance of at most 1.5%. Sensitivity analyses using different values for the bootstrap and genetic distance were performed to study the reproducibility of the clustering. RESULTS Of the 156 participants included in NOVA between July 2015 and April 2021, 134 individuals for whom baseline characteristics and genotypic resistance data at baseline were available could be included. We identified 10 clusters, but the majority of persons (111/134) were not part of a cluster, suggesting mainly independent transmission events. CONCLUSION Mainly independent transmission events among a study population consisting predominantly of MSM in a low-incidence high-resource setting is likely the result of active AEHI case finding and direct start of treatment, and the roll-out over recent years of preventive measures such as preexposure prophylaxis.
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Bhebhe L, Moyo S, Gaseitsiwe S, Pretorius-Holme M, Yankinda EK, Manyake K, Kgathi C, Mmalane M, Lebelonyane R, Gaolathe T, Bachanas P, Ussery F, Letebele M, Makhema J, Wirth KE, Lockman S, Essex M, Novitsky V, Ragonnet-Cronin M. Epidemiological and viral characteristics of undiagnosed HIV infections in Botswana. BMC Infect Dis 2022; 22:710. [PMID: 36031617 PMCID: PMC9420270 DOI: 10.1186/s12879-022-07698-4] [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: 03/14/2022] [Accepted: 08/17/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
HIV-1 is endemic in Botswana. The country’s primary challenge is identifying people living with HIV who are unaware of their status. We evaluated factors associated with undiagnosed HIV infection using HIV-1 phylogenetic, behavioural, and demographic data.
Methods
As part of the Botswana Combination Prevention Project, 20% of households in 30 villages were tested for HIV and followed from 2013 to 2018. A total of 12,610 participants were enrolled, 3596 tested HIV-positive at enrolment, and 147 participants acquired HIV during the trial. Extensive socio-demographic and behavioural data were collected from participants and next-generation sequences were generated for HIV-positive cases. We compared three groups of participants: (1) those previously known to be HIV-positive at enrolment (n = 2995); (2) those newly diagnosed at enrolment (n = 601) and (3) those who tested HIV-negative at enrolment but tested HIV-positive during follow-up (n = 147). We searched for differences in demographic and behavioural factors between known and newly diagnosed group using logistic regression. We also compared the topology of each group in HIV-1 phylogenies and used a genetic diversity-based algorithm to classify infections as recent (< 1 year) or chronic (≥ 1 year).
Results
Being male (aOR = 2.23) and younger than 35 years old (aOR = 8.08) was associated with undiagnosed HIV infection (p < 0.001), as was inconsistent condom use (aOR = 1.76). Women were more likely to have undiagnosed infections if they were married, educated, and tested frequently. For men, being divorced increased their risk. The genetic diversity-based algorithm classified most incident infections as recent (75.0%), but almost none of known infections (2.0%). The estimated proportion of recent infections among new diagnoses was 37.0% (p < 0.001).
Conclusion
Our results indicate that those with undiagnosed infections are likely to be young men and women who do not use condoms consistently. Among women, several factors were predictive: being married, educated, and testing frequently increased risk. Men at risk were more difficult to delineate. A sizeable proportion of undiagnosed infections were recent based on a genetic diversity-based classifier. In the era of “test and treat all”, pre-exposure prophylaxis may be prioritized towards individuals who self-identify or who can be identified using these predictors in order to halt onward transmission in time.
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Reeves I, Cromarty B, Deayton J, Dhairyawan R, Kidd M, Taylor C, Thornhill J, Tickell-Painter M, van Halsema C. British HIV Association guidelines for the management of HIV-2 2021. HIV Med 2021; 22 Suppl 4:1-29. [PMID: 34927347 DOI: 10.1111/hiv.13204] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Iain Reeves
- Consultant in HIV Medicine, Homerton University Hospital NHS Trust, London, UK
| | | | - Jane Deayton
- Clinical Senior Lecturer in HIV, Barts and the London, Queen Mary University of London, London, UK
| | - Rageshri Dhairyawan
- Consultant in Sexual Health and HIV Medicine, Barts Health NHS Trust, London, UK
| | - Mike Kidd
- Consultant Virologist, National Infection Service, Public Health England, UK
| | - Chris Taylor
- Consultant Physician Sexual Health and HIV, Kings College Hospital, London, UK
| | - John Thornhill
- Consultant in Sexual Health and HIV Medicine, Barts Health NHS Trust, London, UK
| | - Maya Tickell-Painter
- Specialist Registrar in Infectious Diseases and Microbiology, Manchester University NHS Foundation Trust, Manchester, UK
| | - Clare van Halsema
- Consultant in Infectious Diseases, North Manchester General Hospital, Manchester, UK
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Ragonnet-Cronin M, Golubchik T, Moyo S, Fraser C, Essex M, Novitsky V, Volz E. HIV genetic diversity informs stage of HIV-1 infection among patients receiving antiretroviral therapy in Botswana. J Infect Dis 2021; 225:1330-1338. [PMID: 34077517 PMCID: PMC9016439 DOI: 10.1093/infdis/jiab293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 06/01/2021] [Indexed: 12/20/2022] Open
Abstract
Background Human immunodeficiency virus (HIV)-1 genetic diversity increases during infection and can help infer the time elapsed since infection. However, the effect of antiretroviral treatment (ART) on the inference remains unknown. Methods Participants with estimated duration of HIV-1 infection based on repeated testing were sourced from cohorts in Botswana (n = 1944). Full-length HIV genome sequencing was performed from proviral deoxyribonucleic acid. We optimized a machine learning model to classify infections as < or >1 year based on viral genetic diversity, demographic, and clinical data. Results The best predictive model included variables for genetic diversity of HIV-1 gag, pol, and env, viral load, age, sex, and ART status. Most participants were on ART. Balanced accuracy was 90.6% (95% confidence interval, 86.7%–94.1%). We tested the algorithm among newly diagnosed participants with or without documented negative HIV tests. Among those without records, those who self-reported a negative HIV test within <1 year were more frequently classified as recent than those who reported a test >1 year previously. There was no difference in classification between those self-reporting a negative HIV test <1 year, whether or not they had a record. Conclusions These results indicate that recency of HIV-1 infection can be inferred from viral sequence diversity even among patients on suppressive ART.
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Affiliation(s)
- Manon Ragonnet-Cronin
- MRC Centre for Global Infectious Diseases Analysis, Imperial College London, London W2 1PG, UK
| | - Tanya Golubchik
- Big Data Institute, University of Oxford, Oxford OX3 7LF, UK
| | | | | | - Max Essex
- Botswana Harvard AIDS Initiative, Gaborone, Botswana.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA FXB 402, USA
| | - Vlad Novitsky
- Botswana Harvard AIDS Initiative, Gaborone, Botswana.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA FXB 402, USA.,Brown University, Providence RI 02912, USA
| | - Erik Volz
- MRC Centre for Global Infectious Diseases Analysis, Imperial College London, London W2 1PG, UK
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Visseaux B, Assoumou L, Mahjoub N, Grude M, Trabaud MA, Raymond S, Wirden M, Morand-Joubert L, Roussel C, Montes B, Bocket L, Fafi-Kremer S, Amiel C, De Monte A, Stefic K, Pallier C, Tumiotto C, Maillard A, Vallet S, Ferre V, Bouvier-Alias M, Dina J, Signori-Schmuck A, Carles MJ, Plantier JC, Meyer L, Descamps D, Chaix ML. Surveillance of HIV-1 primary infections in France from 2014 to 2016: toward stable resistance, but higher diversity, clustering and virulence? J Antimicrob Chemother 2021; 75:183-193. [PMID: 31641777 DOI: 10.1093/jac/dkz404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/19/2019] [Accepted: 08/23/2019] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVES Patients with primary HIV-1 infection (PHI) are a particular population, giving important insight about ongoing evolution of transmitted drug resistance-associated mutation (TDRAM) prevalence, HIV diversity and clustering patterns. We describe these evolutions of PHI patients diagnosed in France from 2014 to 2016. METHODS A total of 1121 PHI patients were included. TDRAMs were characterized using the 2009 Stanford list and the French ANRS algorithm. Viral subtypes and recent transmission clusters (RTCs) were also determined. RESULTS Patients were mainly MSM (70%) living in the Paris area (42%). TDRAMs were identified among 10.8% of patients and rose to 18.6% when including etravirine and rilpivirine TDRAMs. Prevalences of PI-, NRTI-, first-generation NNRTI-, second-generation NNRTI- and integrase inhibitor-associated TDRAMs were 2.9%, 5.0%, 4.0%, 9.4% and 5.4%, respectively. In a multivariable analysis, age >40 years and non-R5 tropic viruses were associated with a >2-fold increased risk of TDRAMs. Regarding HIV diversity, subtype B and CRF02_AG (where CRF stands for circulating recombinant form) were the two main lineages (56% and 20%, respectively). CRF02_AG was associated with higher viral load than subtype B (5.83 versus 5.40 log10 copies/mL, P=0.004). We identified 138 RTCs ranging from 2 to 14 patients and including overall 41% from the global population. Patients in RTCs were younger, more frequently born in France and more frequently MSM. CONCLUSIONS Since 2007, the proportion of TDRAMs has been stable among French PHI patients. Non-B lineages are increasing and may be associated with more virulent CRF02_AG strains. The presence of large RTCs highlights the need for real-time cluster identification to trigger specific prevention action to achieve better control of the epidemic.
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Affiliation(s)
- Benoit Visseaux
- IAME, Université de Paris, AP-HP, UMR 1137, INSERM, Virology, Hôpital Bichat, AP-HP, Paris, France.,Centre National de Référence VIH, Paris, France
| | - Lambert Assoumou
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | | | - Maxime Grude
- AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | | | | | - Marc Wirden
- CHU Pitié-Salpêtrière, Virology, Paris, France
| | - Laurence Morand-Joubert
- AP-HP, Hôpital Saint-Antoine, Laboratoire de virologie, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, (iPLESP), Paris, France
| | | | | | | | | | | | | | - Karl Stefic
- INSERM U1259, Université de Tours, CHU Tours, Virology, Tours, France
| | | | | | | | | | | | | | | | | | | | - Jean-Christophe Plantier
- Normandie University, UNIROUEN Rouen, EA2656, Rouen University Hospital, Virology, Rouen, France
| | - Laurence Meyer
- INSERM SC10 US19, Villejuif, INSERM CESP U1018, Université Paris Sud, Université Paris Saclay, France
| | - Diane Descamps
- IAME, Université de Paris, AP-HP, UMR 1137, INSERM, Virology, Hôpital Bichat, AP-HP, Paris, France.,Centre National de Référence VIH, Paris, France
| | - Marie-Laure Chaix
- Centre National de Référence VIH, Paris, France.,Hopital Saint-Louis, Virology, Paris, France.,Université de Paris, INSERM U944, Paris, France
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Molecular Transmission Dynamics of Primary HIV Infections in Lazio Region, Years 2013-2020. Viruses 2021; 13:v13020176. [PMID: 33503987 PMCID: PMC7911907 DOI: 10.3390/v13020176] [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: 12/02/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
Molecular investigation of primary HIV infections (PHI) is crucial to describe current dynamics of HIV transmission. Aim of the study was to investigate HIV transmission clusters (TC) in PHI referred during the years 2013–2020 to the National Institute for Infectious Diseases in Rome (INMI), that is the Lazio regional AIDS reference centre, and factors possibly associated with inclusion in TC. These were identified by phylogenetic analysis, based on population sequencing of pol; a more in depth analysis was performed on TC of B subtype, using ultra-deep sequencing (UDS) of env. Of 270 patients diagnosed with PHI during the study period, 229 were enrolled (median follow-up 168 (IQR 96–232) weeks). Median age: 39 (IQR 32–48) years; 94.8% males, 86.5% Italians, 83.4% MSM, 56.8% carrying HIV-1 subtype B. Of them, 92.6% started early treatment within a median of 4 (IQR 2–7) days after diagnosis; median time to sustained suppression was 20 (IQR 8–32) weeks. Twenty TC (median size 3, range 2–9 individuals), including 68 patients, were identified. A diagnosis prior to 2015 was the unique factor associated with inclusion in a TC. Added value of UDS was the identification of shared quasispecies components in transmission pairs within TC.
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Zheng M, Yu M, Cheng S, Zhou N, Ning T, Li L, Zhao F, Zhao X, Zhu J, Jiang G. Characteristics of HIV-1 molecular transmission networks and drug resistance among men who have sex with men in Tianjin, China (2014-2018). Virol J 2020; 17:169. [PMID: 33143744 PMCID: PMC7640427 DOI: 10.1186/s12985-020-01441-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/27/2020] [Indexed: 11/25/2022] Open
Abstract
Background In Tianjin, China, there is a relatively high prevalence of HIV in men who have sex with men (MSM). The number of HIV cases in Tianjin is also increasing. We investigated the HIV molecular transmission network, genetic tropisms, and drug resistance mutations in Tianjin.
Methods Blood samples were collected from 510 newly diagnosed antiretroviral therapy (ART)-naïve HIV-1-infected subjects among MSM in Tianjin. Partial pol and env genes were sequenced and used for phylogenetic, genetic tropism, and genotypic drug resistance analyses. Molecular clusters were identified with 1.5% genetic distance and 90% bootstrap support. Results Among the 436 HIV-1 pol sequences obtained from the study participants, various genotypes were identified, including CRF01_AE (56.9%), CRF07_BC (27.8%), B (7.3%), CRF55_01B (4.1%), unique recombinant forms (URFs) (3.7%), and CRF59_01B (0.2%). A higher prevalence of X4 viruses was observed in individuals infected with CRF55_01B (56.3%) and CRF01_AE (46.2%) than with other subtypes. Of all 110 sequences in the 36 clusters, 62 (56.4%) were observed in 23 CRF01_AE clusters and 18 (16.4%) in four CRF07_BC clusters. Eight sequences clustered with at least one other shared the same drug resistance mutation (DRM). In different cluster sizes, the distributions of individuals by age, presence of sexually transmitted disease, and presence of DRMs, were significantly different. Conclusion We revealed the characteristics of HIV molecular transmission, tropism, and DRMs of ART-naïve HIV-infected individuals among the MSM population in Tianjin. Identifying infected persons at risk of transmission is necessary for proposing counseling and treating these patients to reduce the risk of HIV transmission.
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Affiliation(s)
- Minna Zheng
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Maohe Yu
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Shaohui Cheng
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Ning Zhou
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Tielin Ning
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Long Li
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Fangning Zhao
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Xuan Zhao
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Jingjin Zhu
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Guohong Jiang
- Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China.
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9
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Volz EM, Le Vu S, Ratmann O, Tostevin A, Dunn D, Orkin C, O'Shea S, Delpech V, Brown A, Gill N, Fraser C. Molecular Epidemiology of HIV-1 Subtype B Reveals Heterogeneous Transmission Risk: Implications for Intervention and Control. J Infect Dis 2019; 217:1522-1529. [PMID: 29506269 PMCID: PMC5913615 DOI: 10.1093/infdis/jiy044] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 01/22/2018] [Indexed: 11/25/2022] Open
Abstract
Background The impact of HIV pre-exposure prophylaxis (PrEP) depends on infections averted by protecting vulnerable individuals as well as infections averted by preventing transmission by those who would have been infected if not receiving PrEP. Analysis of HIV phylogenies reveals risk factors for transmission, which we examine as potential criteria for allocating PrEP. Methods We analyzed 6912 HIV-1 partial pol sequences from men who have sex with men (MSM) in the United Kingdom combined with global reference sequences and patient-level metadata. Population genetic models were developed that adjust for stage of infection, global migration of HIV lineages, and changing incidence of infection through time. Models were extended to simulate the effects of providing susceptible MSM with PrEP. Results We found that young age <25 years confers higher risk of HIV transmission (relative risk = 2.52 [95% confidence interval, 2.32–2.73]) and that young MSM are more likely to transmit to one another than expected by chance. Simulated interventions indicate that 4-fold more infections can be averted over 5 years by focusing PrEP on young MSM. Conclusions Concentrating PrEP doses on young individuals can avert more infections than random allocation.
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Affiliation(s)
- Erik M Volz
- Department of Infectious Disease Epidemiology and the National Institute for Health Research Health Protection Research Unit on Modeling Methodology, Imperial College London
| | - Stephane Le Vu
- Department of Infectious Disease Epidemiology and the National Institute for Health Research Health Protection Research Unit on Modeling Methodology, Imperial College London
| | - Oliver Ratmann
- Department of Infectious Disease Epidemiology and the National Institute for Health Research Health Protection Research Unit on Modeling Methodology, Imperial College London
| | - Anna Tostevin
- Institute for Global Health, University College London
| | - David Dunn
- Institute for Global Health, University College London
| | | | - Siobhan O'Shea
- Infection Sciences, Viapath Analytics, Guy's and St Thomas' NHS Foundation Trust, London
| | | | | | | | - Christophe Fraser
- Li Ka Shing Centre for Health Information and Discovery, Oxford University, United Kingdom
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Van Der Elst EM, Kombo B, Mugo P, Thiong’o A, Kanungi J, Wahome E, Chirro O, Graham SM, Operario D, Sanders EJ. Adjustment to acute or early HIV-1 infection diagnosis to prompt linkage to care and ART initiation: qualitative insights from coastal Kenya. PSYCHOL HEALTH MED 2019; 24:631-641. [PMID: 30468392 PMCID: PMC6425912 DOI: 10.1080/13548506.2018.1549736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 11/13/2018] [Indexed: 01/06/2023]
Abstract
Diagnosing and treating patients with acute or early HIV-1 infection (AEHI) is an important strategy to prevent HIV-1 transmission. We used qualitative methods to understand factors that facilitate adjustment to AEHI diagnosis, prompt linkage to care and initiation of antiretroviral treatment (ART). Twenty-three AEHI patients (12 women, 11 men) included 18 participants identified at health facilities, and 5 participants identified in a sex worker cohort. Of these, 17 participants (9 women, 8 men) participated in qualitative interviews about their AEHI status 2 weeks after diagnosis. Thirteen participants (7 women, 6 men) returned for a second interview 12 weeks after diagnosis. Interviews explored participants' experiences at the time of and following their diagnosis, and examined perceptions about ART initiation and behavior change recommendations, including disclosure and partner notification. A grounded theory framework was used for analysis, eliciting three important needs that should be addressed for AEHI patients: 1) the need to better understand AEHI and accept one's status; 2) the need to develop healthy strategies and adjust to the reality of AEHI status; and 3) the need to protect self and others through ART initiation, adherence, safer sex, and disclosure. A preliminary conceptual framework to guide further intervention and research with AEHI populations is proposed.
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Affiliation(s)
- EM Van Der Elst
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Global Health, Academic Medical Centre, University of Amsterdam, Amsterdam, Netherlands
| | - B Kombo
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - P Mugo
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - A Thiong’o
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - J Kanungi
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - E Wahome
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - O Chirro
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - SM Graham
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- Departments of Medicine, Global Health, and Epidemiology, University of Washington, Seattle, WA, USA
| | - D Operario
- Department of Behaviour and Social Sciences, Brown University School of Public Health, RI, USA
| | - EJ Sanders
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Global Health, Academic Medical Centre, University of Amsterdam, Amsterdam, Netherlands
- Centre for Topical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Dimitrov D, Wood D, Ulrich A, Swan DA, Adamson B, Lama JR, Sanchez J, Duerr A. Projected effectiveness of HIV detection during early infection and rapid ART initiation among MSM and transgender women in Peru: A modeling study. Infect Dis Model 2019; 4:73-82. [PMID: 31025025 PMCID: PMC6475714 DOI: 10.1016/j.idm.2019.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 04/01/2019] [Accepted: 04/03/2019] [Indexed: 12/01/2022] Open
Abstract
Background The Sabes study, a treatment as prevention intervention in Peru, tested the hypothesis that initiating antiretroviral therapy (ART) early in HIV infection when viral load is high, would markedly reduce onward HIV transmission among high-risk men who have sex with men (MSM) and transgender women (TW). We investigated the potential population-level benefits of detection of HIV early after acquisition and rapid initiation of ART. Methods We designed a transmission dynamic model to simulate the HIV epidemic among MSM and TW in Peru, calibrated to data on HIV prevalence and ART coverage from 2004 to 2011. We assessed the impact of an intervention starting in 2018 in which up to 50% of the new infections were diagnosed within three months of acquisition and initiated on ART within 1 month of diagnosis. We estimated the impact of the intervention over 20 years using the cumulative prevented fraction of new HIV infections compared to scenarios without intervention. Findings Our model suggests that only 19% of the infected MSM and TW are virally suppressed in 2018 and 35%-40% of the new HIV infections are transmitted from contacts with acutely-infected partners. An intervention reaching 10% of all acutely infected MSM and TW is projected to prevent 13.3% [Uncertainty interval: 11.9%-14.3%] of the new infections over 20 years and reduce HIV incidence in 2038 by 24%. Reaching 50% of all acutely infected MSM and TW will increase the prevalence of viral suppression in 2038 to 59% and prevent 41% of expected infections over 20 years. Reaching 50% of the high-risk MSM and TW in acute phase would reduce HIV incidence in 2038 by 60% and prevent 36% of new infections between 2018 and 2038. Conclusions Early detection of HIV infections and rapid initiation of ART among MSM is desirable as it would increase the effectiveness of the HIV prevention program in Peru. Targeting high-risk MSM and TW will be highly efficient.
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Affiliation(s)
- Dobromir Dimitrov
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Daniel Wood
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Angela Ulrich
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Global Health, University of Washington, Seattle, WA, USA
| | - David A Swan
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Blythe Adamson
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Comparative Health Outcomes, Policy, & Economics (CHOICE) Institute, University of Washington, Seattle, WA, USA
| | - Javier R Lama
- Asociación Civil Impacta Salud y Educación, Lima, Peru
| | - Jorge Sanchez
- Centro de Investigaciones Tecnológicas, Biomédicas y Medioambientales, Universidad Mayor de San Marcos, Lima, Peru
| | - Ann Duerr
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Global Health, University of Washington, Seattle, WA, USA
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12
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Abstract
OBJECTIVES Molecular epidemiology is applied to various aspects of HIV transmission analyses. With ultradeep sequencing (UDS), in-depth characterization of transmission episodes involving minority variants is permitted. We explored HIV-1 epidemiological linkage and evaluated characteristics of transmission dynamics and transmitted drug resistance (TDR) detection through the added value of UDS. DESIGN HIV pol gene fragments were sequenced by UDS and Sanger sequencing on samples of 70 HIV-1-infected, treatment-naive recently diagnosed MSM. METHODS Pairwise genetic distances and maximum likelihood phylogenies were computed. Transmission events were identified as clades with branch support at least 70% and intraclade genetic difference less than 4.5%. TDR mutations were recognized from the TDR consensus list. Transmission directionality, directness and inoculum size were inferred from tree topologies. RESULTS Both datasets concurred in the identification of seven transmission pairs and one cluster of three patients. With UDS, direction of transmission was inferred in four out of eight chains. Evidence for multiple founder viruses was found in two out of eight chains. No transmission of minority-resistant variants was evidenced. TDR mutations prevalence in protease and reverse transcriptase fragments was 4.3% with Sanger sequencing and 18.6% with UDS. CONCLUSION Although Sanger sequencing and UDS identified the same transmission chains, UDS provided additional information on founder viruses, direction of transmission and levels of TDR. Nevertheless, topology of clusters was not always consistent across gene fragments, calling for a cautious interpretation of the data. Moreover, unobserved intermediary links cannot be excluded. Phylogenetic analysis use as a forensic technique for HIV transmission investigations is risky.
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13
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Ragonnet-Cronin M, Hu YW, Morris SR, Sheng Z, Poortinga K, Wertheim JO. HIV transmission networks among transgender women in Los Angeles County, CA, USA: a phylogenetic analysis of surveillance data. Lancet HIV 2019; 6:e164-e172. [PMID: 30765313 PMCID: PMC6887514 DOI: 10.1016/s2352-3018(18)30359-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 12/30/2022]
Abstract
BACKGROUND Transgender women are among the groups at highest risk for HIV infection, with a prevalence of 27·7% in the USA; and despite this known high risk, undiagnosed infection is common in this population. We set out to identify transgender women and their partners in a molecular transmission network to prioritise public health activities. METHODS Since 2006, HIV protease and reverse transcriptase gene (pol) sequences from drug resistance testing have been reported to the Los Angeles County Department of Public Health and linked to demographic data, gender, and HIV transmission risk factor data for each case in the enhanced HIV/AIDS Reporting System. We reconstructed a molecular transmission network by use of HIV-TRAnsmission Cluster Engine (with a pairwise genetic distance threshold of 0·015 substitutions per site) from the earliest pol sequences from 22 398 unique individuals, including 412 (2%) self-identified transgender women. We examined the possible predictors of clustering with multivariate logistic regression. We characterised the genetically linked partners of transgender women and calculated assortativity (the tendency for people to link to other people with the same attributes) for each transmission risk group. FINDINGS 8133 (36·3%) of 22 398 individuals clustered in the network across 1722 molecular transmission clusters. Transgender women who indicated a sexual risk factor clustered at the highest frequency in the network, with 147 (43%) of 345 being linked to at least one other person (adjusted odds ratio [aOR] 2·0, p=0·0002). Transgender women were assortative in the network (assortativity 0·06, p<0·001), indicating that they tended to link to other transgender women. Transgender women were more likely than expected to link to other transgender women (OR 4·65, p<0·001) and cisgender men who did not identify as men who have sex with men (MSM; OR 1·53, p<0·001). Transgender women were less likely than expected to link to MSM (OR 0·75, p<0·001), despite the high prevalence of HIV among MSM. Transgender women were distributed across 126 clusters, and cisgender individuals linked to one transgender woman were 9·2 times more likely to link to a second transgender woman than other individuals in the surveillance database. Reconstruction of the transmission network is limited by sample availability, but sequences were available for more than 40% of diagnoses. INTERPRETATION Clustering of transgender women and the observed tendency for linkage with cisgender men who did not identify as MSM, shows the potential to use molecular epidemiology both to identify clusters that are likely to include undiagnosed transgender women with HIV and to improve the targeting of public health prevention and treatment services to transgender women. FUNDING California HIV and AIDS Research Program and National Institutes of Health-National Institute of Allergy and Infectious Diseases.
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Affiliation(s)
- Manon Ragonnet-Cronin
- Department of Medicine, University of California, San Diego, CA, USA; MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
| | - Yunyin W Hu
- Division of HIV and STD Programs, Department of Public Health, Los Angeles, CA, USA
| | - Sheldon R Morris
- Department of Medicine, University of California, San Diego, CA, USA
| | - Zhijuan Sheng
- Division of HIV and STD Programs, Department of Public Health, Los Angeles, CA, USA
| | - Kathleen Poortinga
- Division of HIV and STD Programs, Department of Public Health, Los Angeles, CA, USA
| | - Joel O Wertheim
- Department of Medicine, University of California, San Diego, CA, USA
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14
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Churchill D, Waters L, Ahmed N, Angus B, Boffito M, Bower M, Dunn D, Edwards S, Emerson C, Fidler S, Fisher M, Horne R, Khoo S, Leen C, Mackie N, Marshall N, Monteiro F, Nelson M, Orkin C, Palfreeman A, Pett S, Phillips A, Post F, Pozniak A, Reeves I, Sabin C, Trevelion R, Walsh J, Wilkins E, Williams I, Winston A. British HIV Association guidelines for the treatment of HIV-1-positive adults with antiretroviral therapy 2015. HIV Med 2018; 17 Suppl 4:s2-s104. [PMID: 27568911 DOI: 10.1111/hiv.12426] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | | | | | | | | | - Mark Bower
- Chelsea and Westminster Hospital, London, UK
| | | | - Simon Edwards
- Central and North West London NHS Foundation Trust, UK
| | | | - Sarah Fidler
- Imperial College School of Medicine at St Mary's, London, UK
| | | | | | | | | | | | | | | | - Mark Nelson
- Chelsea and Westminster Hospital NHS Foundation Trust, London, UK
| | | | | | | | | | | | - Anton Pozniak
- Chelsea and Westminster Hospital NHS Foundation Trust, London, UK
| | | | - Caroline Sabin
- Royal Free and University College Medical School, London, UK
| | | | - John Walsh
- Imperial College Healthcare NHS Trust, London, UK
| | | | - Ian Williams
- Royal Free and University College Medical School, London, UK
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15
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Pérez-Losada M, Castel AD, Lewis B, Kharfen M, Cartwright CP, Huang B, Maxwell T, Greenberg AE, Crandall KA. Characterization of HIV diversity, phylodynamics and drug resistance in Washington, DC. PLoS One 2017; 12:e0185644. [PMID: 28961263 PMCID: PMC5621693 DOI: 10.1371/journal.pone.0185644] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 09/16/2017] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Washington DC has a high burden of HIV with a 2.0% HIV prevalence. The city is a national and international hub potentially containing a broad diversity of HIV variants; yet few sequences from DC are available on GenBank to assess the evolutionary history of HIV in the US capital. Towards this general goal, here we analyze extensive sequence data and investigate HIV diversity, phylodynamics, and drug resistant mutations (DRM) in DC. METHODS Molecular HIV-1 sequences were collected from participants infected through 2015 as part of the DC Cohort, a longitudinal observational study of HIV+ patients receiving care at 13 DC clinics. Sequences were paired with Cohort demographic, risk, and clinical data and analyzed using maximum likelihood, Bayesian and coalescent approaches of phylogenetic, network and population genetic inference. We analyzed 601 sequences from 223 participants for int (~864 bp) and 2,810 sequences from 1,659 participants for PR/RT (~1497 bp). RESULTS Ninety-nine and 94% of the int and PR/RT sequences, respectively, were identified as subtype B, with 14 non-B subtypes also detected. Phylodynamic analyses of US born infected individuals showed that HIV population size varied little over time with no significant decline in diversity. Phylogenetic analyses grouped 13.5% of the int sequences into 14 clusters of 2 or 3 sequences, and 39.0% of the PR/RT sequences into 203 clusters of 2-32 sequences. Network analyses grouped 3.6% of the int sequences into 4 clusters of 2 sequences, and 10.6% of the PR/RT sequences into 76 clusters of 2-7 sequences. All network clusters were detected in our phylogenetic analyses. Higher proportions of clustered sequences were found in zip codes where HIV prevalence is highest (r = 0.607; P<0.00001). We detected a high prevalence of DRM for both int (17.1%) and PR/RT (39.1%), but only 8 int and 12 PR/RT amino acids were identified as under adaptive selection. We observed a significant (P<0.0001) association between main risk factors (men who have sex with men and heterosexuals) and genotypes in the five well-supported clusters with sufficient sample size for testing. DISCUSSION Pairing molecular data with clinical and demographic data provided novel insights into HIV population dynamics in Washington, DC. Identification of populations and geographic locations where clustering occurs can inform and complement active surveillance efforts to interrupt HIV transmission.
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Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Ashburn, VA, United States of America
- CIBIO-InBIO, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, The George Washington University, Washington, DC, United States of America
| | - Amanda D. Castel
- Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, The George Washington University, Washington, DC, United States of America
| | - Brittany Lewis
- Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, The George Washington University, Washington, DC, United States of America
| | - Michael Kharfen
- District of Columbia Department of Health, Washington, DC, United States of America
| | | | - Bruce Huang
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Ashburn, VA, United States of America
| | - Taylor Maxwell
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Ashburn, VA, United States of America
| | - Alan E. Greenberg
- Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, The George Washington University, Washington, DC, United States of America
| | - Keith A. Crandall
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Ashburn, VA, United States of America
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16
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Rutstein SE, Ananworanich J, Fidler S, Johnson C, Sanders EJ, Sued O, Saez-Cirion A, Pilcher CD, Fraser C, Cohen MS, Vitoria M, Doherty M, Tucker JD. Clinical and public health implications of acute and early HIV detection and treatment: a scoping review. J Int AIDS Soc 2017; 20:21579. [PMID: 28691435 PMCID: PMC5515019 DOI: 10.7448/ias.20.1.21579] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 05/29/2017] [Indexed: 01/13/2023] Open
Abstract
INTRODUCTION The unchanged global HIV incidence may be related to ignoring acute HIV infection (AHI). This scoping review examines diagnostic, clinical, and public health implications of identifying and treating persons with AHI. METHODS We searched PubMed, in addition to hand-review of key journals identifying research pertaining to AHI detection and treatment. We focused on the relative contribution of AHI to transmission and the diagnostic, clinical, and public health implications. We prioritized research from low- and middle-income countries (LMICs) published in the last fifteen years. RESULTS AND DISCUSSION Extensive AHI research and limited routine AHI detection and treatment have begun in LMIC. Diagnostic challenges include ease-of-use, suitability for application and distribution in LMIC, and throughput for high-volume testing. Risk score algorithms have been used in LMIC to screen for AHI among individuals with behavioural and clinical characteristics more often associated with AHI. However, algorithms have not been implemented outside research settings. From a clinical perspective, there are substantial immunological and virological benefits to identifying and treating persons with AHI - evading the irreversible damage to host immune systems and seeding of viral reservoirs that occurs during untreated acute infection. The therapeutic benefits require rapid initiation of antiretrovirals, a logistical challenge in the absence of point-of-care testing. From a public health perspective, AHI diagnosis and treatment is critical to: decrease transmission via viral load reduction and behavioural interventions; improve pre-exposure prophylaxis outcomes by avoiding treatment initiation for HIV-seronegative persons with AHI; and, enhance partner services via notification for persons recently exposed or likely transmitting. CONCLUSIONS There are undeniable clinical and public health benefits to AHI detection and treatment, but also substantial diagnostic and logistical barriers to implementation and scale-up. Effective early ART initiation may be critical for HIV eradication efforts, but widespread use in LMIC requires simple and accurate diagnostic tools. Implementation research is critical to facilitate sustainable integration of AHI detection and treatment into existing health systems and will be essential for prospective evaluation of testing algorithms, point-of-care diagnostics, and efficacious and effective first-line regimens.
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Affiliation(s)
- Sarah E. Rutstein
- Department of Health Policy and Management, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jintanat Ananworanich
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Sarah Fidler
- Department of Medicine, Imperial College London, London, UK
| | - Cheryl Johnson
- HIV Department, World Health Organization, Geneva, Switzerland
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK
| | - Eduard J. Sanders
- Department of Global Health, University of Amsterdam, Amsterdam, The Netherlands
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Omar Sued
- Fundación Huésped, Buenos Aires, Argentina
| | - Asier Saez-Cirion
- Institut Pasteur, HIV Inflammation and Persistance Unit, Paris, France
| | | | - Christophe Fraser
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Myron S. Cohen
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Marco Vitoria
- HIV Department, World Health Organization, Geneva, Switzerland
| | - Meg Doherty
- HIV Department, World Health Organization, Geneva, Switzerland
| | - Joseph D. Tucker
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Project-China, Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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17
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Ratmann O, van Sighem A, Bezemer D, Gavryushkina A, Jurriaans S, Wensing A, de Wolf F, Reiss P, Fraser C. Sources of HIV infection among men having sex with men and implications for prevention. Sci Transl Med 2016; 8:320ra2. [PMID: 26738795 DOI: 10.1126/scitranslmed.aad1863] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
New HIV diagnoses among men having sex with men (MSM) have not decreased appreciably in most countries, even though care and prevention services have been scaled up substantially in the past 20 years. To maximize the impact of prevention strategies, it is crucial to quantify the sources of transmission at the population level. We used viral sequence and clinical patient data from one of Europe's nationwide cohort studies to estimate probable sources of transmission for 617 recently infected MSM. Seventy-one percent of transmissions were from undiagnosed men, 6% from men who had initiated antiretroviral therapy (ART), 1% from men with no contact to care for at least 18 months, and 43% from those in their first year of infection. The lack of substantial reductions in incidence among Dutch MSM is not a result of ineffective ART provision or inadequate retention in care. In counterfactual modeling scenarios, 19% of these past cases could have been averted with current annual testing coverage and immediate ART to those testing positive. Sixty-six percent of these cases could have been averted with available antiretrovirals (immediate ART provided to all MSM testing positive, and preexposure antiretroviral prophylaxis taken by half of all who test negative for HIV), but only if half of all men at risk of transmission had tested annually. With increasing sequence coverage, molecular epidemiological analyses can be a key tool to direct HIV prevention strategies to the predominant sources of infection, and help send HIV epidemics among MSM into a decisive decline.
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Affiliation(s)
- Oliver Ratmann
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W21PG, UK.
| | - Ard van Sighem
- Stichting HIV Monitoring, 1105 BD Amsterdam, the Netherlands
| | - Daniela Bezemer
- Stichting HIV Monitoring, 1105 BD Amsterdam, the Netherlands
| | | | - Suzanne Jurriaans
- Department of Medical Microbiology, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Annemarie Wensing
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Frank de Wolf
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W21PG, UK
| | - Peter Reiss
- Stichting HIV Monitoring, 1105 BD Amsterdam, the Netherlands. Department of Global Health, Academic Medical Center, 1105 BM Amsterdam, the Netherlands
| | - Christophe Fraser
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W21PG, UK
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18
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Milam J, Morris S, Jain S, Sun X, Dubé MP, Daar ES, Jimenez G, Haubrich R. Randomized Controlled Trial of an Internet Application to Reduce HIV Transmission Behavior Among HIV Infected Men Who have Sex with Men. AIDS Behav 2016; 20:1173-1181. [PMID: 26487300 PMCID: PMC4838553 DOI: 10.1007/s10461-015-1215-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We conducted a prospective, randomized controlled trial of an internet-based safer-sex intervention to reduce HIV transmission risk behaviors. HIV-infected men who have sex with men (n = 179) were randomized to receive a monthly internet survey alone or a monthly survey plus tailored risk reduction messages over 12 months. The primary outcome was the cumulative sexually transmitted infection (STI) incidence over 12 months. Secondary outcomes included self-reported unprotected sex with an at risk partner and disclosure of HIV status to partners. In a modified intent to treat analysis, there was no difference in 12-month STI incidence between the intervention and control arms (30 vs. 25 %, respectively; p = 0.5). Unprotected sex decreased and disclosure increased over time in both study arms. These improvements suggest that addition of the risk-reduction messages provided little benefit beyond the self-monitoring of risky behavior via regular self-report risk behavior assessments (as was done in both study arms).
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Affiliation(s)
- Joel Milam
- Keck School of Medicine, University of Southern California, 2001 Soto Building, MC9239, Los Angeles, CA 90032, USA
| | | | - Sonia Jain
- University of California, San Diego, CA, USA
| | | | - Michael P. Dubé
- Keck School of Medicine, University of Southern California, 2001 Soto Building, MC9239, Los Angeles, CA 90032, USA
| | - Eric S. Daar
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Long Beach, CA, USA
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19
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Fidler S, Fox J. Primary HIV infection: a medical and public health emergency requiring rapid specialist management. Clin Med (Lond) 2016; 16:180-3. [PMID: 27037390 PMCID: PMC4952974 DOI: 10.7861/clinmedicine.16-2-180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Primary HIV infection (PHI) refers to the first six months following HIV acquisition and represents a unique opportunity for expedited diagnosis, and consideration of rapid antiretroviral therapy (ART) initiation to improve immune function, reduce the size of the viral reservoir and limit the risk of onward viral transmission. Failure to diagnose and rapidly treat individuals with PHI has significant individual and public health implications. The Strategic Timing of AntiRetroviral Treatment trial recently identified a clinical benefit of immediate ART over deferral of treatment according to CD4 count threshold, and has led to rapid changes in World Health Organization and specialist national guidelines. For all individuals living with HIV, the offer of immediate therapy irrespective of CD4 count is now recommended. This paper summarises the presentation and management of PHI, incorporating current research and guideline changes and discusses the role of PHI in onward transmission.
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Affiliation(s)
| | - Julie Fox
- Guys and St Thomas' NHS Trust, London, UK
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21
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Montoya JL, Cattie J, Morgan E, Woods SP, Cherner M, Moore DJ, Atkinson JH, Grant I. The impact of age, HIV serostatus and seroconversion on methamphetamine use. THE AMERICAN JOURNAL OF DRUG AND ALCOHOL ABUSE 2016; 42:168-77. [PMID: 26837461 DOI: 10.3109/00952990.2015.1114625] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Characterizing methamphetamine use in relation to age, HIV serostatus and seroconversion is pertinent given the increasingly older age of the population with HIV and the intertwined epidemics of methamphetamine use and HIV. OBJECTIVES Study aims were to investigate whether (i) methamphetamine use differs by age and HIV serostatus, and (ii) receiving an HIV diagnosis impacts methamphetamine use among younger and older persons with HIV. METHODS This study examined methamphetamine use characteristics among 217 individuals with a lifetime methamphetamine dependence diagnosis who completed an in-person study assessment. RESULTS Multivariable regressions revealed that HIV serostatus uniquely attenuates methamphetamine use, such that persons with HIV report a smaller cumulative quantity (β = -0.16, p = 0.01) and a fewer number of days (β = -0.18, p = 0.004) of methamphetamine use than persons without HIV. Among the HIV+ sample, all participants persisted in methamphetamine use after receiving an HIV diagnosis, with about 20% initiating use after seroconversion. Repeated measures analysis of variance indicated that density of methamphetamine use (i.e. grams per day used) was greater among the younger, relative to the older, HIV+ group (p = 0.02), and increased for both age groups following seroconversion (p < 0.001). CONCLUSION These analyses indicate that although HIV serostatus may attenuate methamphetamine use behaviors, many people with HIV initiate, or persist in, methamphetamine use after receiving an HIV diagnosis. These findings raise the question of whether tailoring of prevention and intervention strategies might reduce the impact of methamphetamine and HIV across the age continuum.
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Affiliation(s)
- Jessica L Montoya
- a Clinical Psychology, San Diego State University/University of California, San Diego Joint Doctoral Program , San Diego , CA , USA
| | - Jordan Cattie
- a Clinical Psychology, San Diego State University/University of California, San Diego Joint Doctoral Program , San Diego , CA , USA
| | - Erin Morgan
- b Translational Methamphetamine AIDS Research Center, Department of Psychiatry , School of Medicine, University of California, San Diego , La Jolla , CA , USA
| | - Steven Paul Woods
- b Translational Methamphetamine AIDS Research Center, Department of Psychiatry , School of Medicine, University of California, San Diego , La Jolla , CA , USA
| | - Mariana Cherner
- b Translational Methamphetamine AIDS Research Center, Department of Psychiatry , School of Medicine, University of California, San Diego , La Jolla , CA , USA
| | - David J Moore
- b Translational Methamphetamine AIDS Research Center, Department of Psychiatry , School of Medicine, University of California, San Diego , La Jolla , CA , USA
| | - J Hampton Atkinson
- b Translational Methamphetamine AIDS Research Center, Department of Psychiatry , School of Medicine, University of California, San Diego , La Jolla , CA , USA.,c VA San Diego Healthcare System , San Diego , CA , USA
| | - Igor Grant
- b Translational Methamphetamine AIDS Research Center, Department of Psychiatry , School of Medicine, University of California, San Diego , La Jolla , CA , USA
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- c VA San Diego Healthcare System , San Diego , CA , USA
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22
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Girerd-Genessay I, Baratin D, Ferry T, Chidiac C, Ronin V, Vanhems P. Higher HIV RNA Viral Load in Recent Patients with Symptomatic Acute HIV Infection in Lyon University Hospitals. PLoS One 2016; 11:e0146978. [PMID: 26799390 PMCID: PMC4723228 DOI: 10.1371/journal.pone.0146978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 12/23/2015] [Indexed: 11/23/2022] Open
Abstract
Introduction Increased human immunodeficiency virus (HIV) virulence at infection has been suggested by a meta-analysis based on viral load and CD4 T lymphocytes (CD4) count during acute infection. This result was obtained after secondary analyses of large databases, facilitating the detection of differences. Similar finding in cohorts of more modest sample size would indicate that the effect could be more substantial. Methods Change from initial CD4 count and HIV viral load after acute HIV infection by calendar year was explored in patients treated at Lyon University hospitals. All patients admitted to our hospitals with acute HIV infection between 1996 and 2013 were included in our study. Initial CD4 count and viral load before the start of anti-retroviral treatment were analyzed. Trends over time were assessed in linear models. Results Initial CD4 count remained similar over time. However, in 2006–2013, initial viral load rose significantly (+1.12 log10/ml/year, p = 0.01). Conclusion Our data, obtained from a single hospital cohort, confirmed findings from a large meta-analysis, showed increased initial viremia at acute HIV infection since 2006 and suggesting potentially higher HIV virulence in recent years.
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Affiliation(s)
- Isabelle Girerd-Genessay
- Infection Control and Epidemiology Unit, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, France
| | - Dominique Baratin
- Infection Control and Epidemiology Unit, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, France
| | - Tristan Ferry
- Department of Infectious Diseases, Hospices Civils de Lyon, Lyon, France
| | - Christian Chidiac
- Department of Infectious Diseases, Hospices Civils de Lyon, Lyon, France
| | - Vincent Ronin
- Infection Control and Epidemiology Unit, Hôpital Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - Philippe Vanhems
- Infection Control and Epidemiology Unit, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, France
- Emerging Pathogens Laboratory, Fondation Mérieux, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, ENS de Lyon, UCBL1, 21, Avenue Tony Garnier, Lyon, 69007, France
- * E-mail:
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Vrbik I, Stephens DA, Roger M, Brenner BG. The Gap Procedure: for the identification of phylogenetic clusters in HIV-1 sequence data. BMC Bioinformatics 2015; 16:355. [PMID: 26538192 PMCID: PMC4634160 DOI: 10.1186/s12859-015-0791-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 10/22/2015] [Indexed: 11/29/2022] Open
Abstract
Background In the context of infectious disease, sequence clustering can be used to provide important insights into the dynamics of transmission. Cluster analysis is usually performed using a phylogenetic approach whereby clusters are assigned on the basis of sufficiently small genetic distances and high bootstrap support (or posterior probabilities). The computational burden involved in this phylogenetic threshold approach is a major drawback, especially when a large number of sequences are being considered. In addition, this method requires a skilled user to specify the appropriate threshold values which may vary widely depending on the application. Results This paper presents the Gap Procedure, a distance-based clustering algorithm for the classification of DNA sequences sampled from individuals infected with the human immunodeficiency virus type 1 (HIV-1). Our heuristic algorithm bypasses the need for phylogenetic reconstruction, thereby supporting the quick analysis of large genetic data sets. Moreover, this fully automated procedure relies on data-driven gaps in sorted pairwise distances to infer clusters, thus no user-specified threshold values are required. The clustering results obtained by the Gap Procedure on both real and simulated data, closely agree with those found using the threshold approach, while only requiring a fraction of the time to complete the analysis. Conclusions Apart from the dramatic gains in computational time, the Gap Procedure is highly effective in finding distinct groups of genetically similar sequences and obviates the need for subjective user-specified values. The clusters of genetically similar sequences returned by this procedure can be used to detect patterns in HIV-1 transmission and thereby aid in the prevention, treatment and containment of the disease. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0791-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Irene Vrbik
- Department of Mathematics & Statistics, McGill University, 805 Sherbrooke Street West, Montreal, H3A 0B9, Canada.
| | - David A Stephens
- Department of Mathematics & Statistics, McGill University, 805 Sherbrooke Street West, Montreal, H3A 0B9, Canada.
| | - Michel Roger
- Centre de recherche du CHUM, 900 rue Saint-Denis Tour Viger, H2X 0A9, Montreal, Canada.
| | - Bluma G Brenner
- Faculty of Surgery (Medicine), McGill University, 1010 Sherbrooke Street West, Montreal, H3A 2R7, Canada. .,McGill University AIDS Centre, Jewish General Hospital, Côte-Sainte-Catherine, Montreal, H3T1E2, Canada.
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Viciana I, González-Domenech CM, Palacios R, Delgado M, Del Arco A, Tellez F, Jarilla F, Fernández S, Clavijo E, Santos J. Clinical, virological and phylogenetic characterization of a multiresistant HIV-1 strain outbreak in naive patients in southern Spain. J Antimicrob Chemother 2015; 71:357-61. [PMID: 26483513 DOI: 10.1093/jac/dkv332] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 09/15/2015] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND We describe the characteristics of an HIV-1 strain with six viral reverse transcriptase mutations (D67N, T69N/D, V118I, V179D, T215S and K219Q), which we have called the Malaga strain. This strain was detected in treatment-naive patients from southern Spain. METHODS The study was undertaken at the Virgen de la Victoria Hospital, Malaga, a reference centre for the study of HIV-1 genotype resistance in Andalusia (the 'Costa del Sol'), Spain. Genotypic resistance testing was done in an automated sequencer. Phylogenetic analysis was performed using a 630 bp region of the reverse transcriptase with the mutations mentioned. RESULTS Between 2007 and 2014, we detected the Malaga strain in 30 treatment-naive patients. All were MSM, seen at five hospitals on the Costa del Sol. In all cases, the HIV-1 was subtype B with viral tropism R5. Phylogenetic analysis based on the reverse transcriptase sequence showed consistent grouping (with a bootstrap value of the common node of 100%) of the isolates that shared the mutation pattern mentioned. This strain has not been detected elsewhere or in previously treated patients. All of the patients treated with first-line combination ART responded. CONCLUSIONS We report a cluster of an HIV-1 strain with multiple resistance mutations that was transmitted over a period of >8 years, affecting 30 naive patients from the same geographical area. The strain was susceptible to first-line combination ART.
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Affiliation(s)
- I Viciana
- UGCI de Enfermedades Infecciosas y Microbiología Clínica, Hospital Virgen de la Victoria, Málaga, Spain Instituto de Investigación de Biomedicina de Málaga (IBIMA), Malaga, Spain
| | | | - R Palacios
- UGCI de Enfermedades Infecciosas y Microbiología Clínica, Hospital Virgen de la Victoria, Málaga, Spain Instituto de Investigación de Biomedicina de Málaga (IBIMA), Malaga, Spain
| | - M Delgado
- UGCI de Enfermedades Infecciosas y Microbiología Clínica, Hospital Regional Carlos Haya, Málaga, Spain
| | - A Del Arco
- UGC de Enfermedades Infecciosas, Hospital Costa del Sol, Marbella, Spain
| | - F Tellez
- UGC de Enfermedades Infecciosas y Microbiología Clínica, Hospital La Línea, AGS Campo de Gibraltar, Cádiz, Spain
| | - F Jarilla
- Servicio de Medicina Interna, Hospital Comarcal de Antequera, Malaga, Spain
| | - S Fernández
- Servicio de Medicina Interna, Hospital Comarcal de la Axarquía, Vélez-Málaga, Spain
| | - E Clavijo
- UGCI de Enfermedades Infecciosas y Microbiología Clínica, Hospital Virgen de la Victoria, Málaga, Spain
| | - J Santos
- UGCI de Enfermedades Infecciosas y Microbiología Clínica, Hospital Virgen de la Victoria, Málaga, Spain Instituto de Investigación de Biomedicina de Málaga (IBIMA), Malaga, Spain
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Brief Report: Recent Infection, Sexually Transmitted Infections, and Transmission Clusters Frequently Observed Among Persons Newly Diagnosed With HIV in San Francisco. J Acquir Immune Defic Syndr 2015; 69:606-9. [PMID: 25967271 DOI: 10.1097/qai.0000000000000681] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
There were 1311 newly diagnosed HIV cases in San Francisco between 2005 and 2011 that were linked to care at publicly funded facilities and had viral sequences available for analysis. Of the 214 cases characterized as recently infected with HIV at the time of diagnosis, 25% had a recent sexually transmitted infection diagnosis (vs. 10% among longer-standing HIV infections, P < 0.001) and 57% were part of a phylogenetic transmission cluster (vs. 42% among longer-standing HIV infection, P < 0.001). The association observed between recent HIV infection and having a sexually transmitted infection diagnosis during the interval overlapping likely HIV acquisition points to potential opportunities to interrupt HIV transmission.
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Cabrera C, Chang L, Stone M, Busch M, Wilson DH. Rapid, Fully Automated Digital Immunoassay for p24 Protein with the Sensitivity of Nucleic Acid Amplification for Detecting Acute HIV Infection. Clin Chem 2015; 61:1372-80. [PMID: 26369787 DOI: 10.1373/clinchem.2015.243287] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 08/14/2015] [Indexed: 11/06/2022]
Abstract
BACKGROUND Nucleic acid testing (NAT) has become the standard for high sensitivity in detecting low levels of virus. However, adoption of NAT can be cost prohibitive in low-resource settings where access to extreme sensitivity could be clinically advantageous for early detection of infection. We report development and preliminary validation of a simple, low-cost, fully automated digital p24 antigen immunoassay with the sensitivity of quantitative NAT viral load (NAT-VL) methods for detection of acute HIV infection. METHODS We developed an investigational 69-min immunoassay for p24 capsid protein for use on a novel digital analyzer on the basis of single-molecule-array technology. We evaluated the assay for sensitivity by dilution of standardized preparations of p24, cultured HIV, and preseroconversion samples. We characterized analytical performance and concordance with 2 NAT-VL methods and 2 contemporary p24 Ag/Ab combination immunoassays with dilutions of viral isolates and samples from the earliest stages of HIV infection. RESULTS Analytical sensitivity was 0.0025 ng/L p24, equivalent to 60 HIV RNA copies/mL. The limit of quantification was 0.0076 ng/L, and imprecision across 10 runs was <10% for samples as low as 0.09 ng/L. Clinical specificity was 95.1%. Sensitivity concordance vs NAT-VL on dilutions of preseroconversion samples and Group M viral isolates was 100%. CONCLUSIONS The digital immunoassay exhibited >4000-fold greater sensitivity than contemporary immunoassays for p24 and sensitivity equivalent to that of NAT methods for early detection of HIV. The data indicate that NAT-level sensitivity for acute HIV infection is possible with a simple, low-cost digital immunoassay.
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Affiliation(s)
| | | | - Mars Stone
- Blood Systems Research Institute, San Francisco, CA
| | - Michael Busch
- Blood Systems Research Institute, San Francisco, CA; University of California, San Francisco, San Francisco, CA
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Suthar AB, Granich RM, Kato M, Nsanzimana S, Montaner JSG, Williams BG. Programmatic Implications of Acute and Early HIV Infection. J Infect Dis 2015; 212:1351-60. [PMID: 26310309 DOI: 10.1093/infdis/jiv430] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 08/18/2015] [Indexed: 02/01/2023] Open
Abstract
Human immunodeficiency virus (HIV) infection includes acute, early, chronic, and late stages. Acute HIV infection lasts approximately 3 weeks and early HIV infection, which includes acute HIV infection, lasts approximately 7 weeks. Many testing and blood screening algorithms detect HIV antibodies about 3 weeks after HIV infection. Incidence estimates are based on results of modeling, cohort studies, surveillance, and/or assays. Viral load is the key modifiable risk factor for HIV transmission and peaks during acute and early HIV infection. Empirical evidence characterizing the impact of acute and early HIV infection on the spread of the HIV epidemic are limited. Time trends of HIV prevalence collected from concentrated and generalized epidemics suggest that acute and early HIV infection may have a limited role in population HIV transmission. Collectively, these data suggest that acute and early HIV infection is relatively short and does not currently require fundamentally different programmatic approaches to manage the HIV/AIDS epidemic in most settings. Research and surveillance will inform which epidemic contexts and phases may require tailored strategies for these stages of HIV infection.
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Affiliation(s)
- Amitabh B Suthar
- South African Centre for Epidemiological Modelling and Analysis, University of Stellenbosch, South Africa
| | - Reuben M Granich
- International Association of Providers of AIDS Care, Washington D.C
| | - Masaya Kato
- World Health Organization Vietnam Country Office, Hanoi
| | | | | | - Brian G Williams
- Wits Reproductive Health Institute, University of the Witwatersrand, Johannesburg, South Africa
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Recent Transmission Clustering of HIV-1 C and CRF17_BF Strains Characterized by NNRTI-Related Mutations among Newly Diagnosed Men in Central Italy. PLoS One 2015; 10:e0135325. [PMID: 26270824 PMCID: PMC4535860 DOI: 10.1371/journal.pone.0135325] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/21/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Increased evidence of relevant HIV-1 epidemic transmission in European countries is being reported, with an increased circulation of non-B-subtypes. Here, we present two recent HIV-1 non-B transmission clusters characterized by NNRTI-related amino-acidic mutations among newly diagnosed HIV-1 infected men, living in Rome (Central-Italy). METHODS Pol and V3 sequences were available at the time of diagnosis for all individuals. Maximum-Likelihood and Bayesian phylogenetic-trees with bootstrap and Bayesian-probability supports defined transmission-clusters. HIV-1 drug-resistance and V3-tropism were also evaluated. RESULTS Among 534 new HIV-1 non-B cases, diagnosed from 2011 to 2014, in Central-Italy, 35 carried virus gathering in two distinct clusters, including 27 HIV-1 C and 8 CRF17_BF subtypes, respectively. Both clusters were centralized in Rome, and their origin was estimated to have been after 2007. All individuals within both clusters were males and 37.1% of them had been recently-infected. While C-cluster was entirely composed by Italian men-who-have-sex-with-men, with a median-age of 34 years (IQR:30-39), individuals in CRF17_BF-cluster were older, with a median-age of 51 years (IQR:48-59) and almost all reported sexual-contacts with men and women. All carried R5-tropic viruses, with evidence of atypical or resistance amino-acidic mutations related to NNRTI-drugs (K103Q in C-cluster, and K101E+E138K in CRF17_BF-cluster). CONCLUSIONS These two epidemiological clusters provided evidence of a strong and recent circulation of C and CRF17_BF strains in central Italy, characterized by NNRTI-related mutations among men engaging in high-risk behaviours. These findings underline the role of molecular epidemiology in identifying groups at increased risk of HIV-1 transmission, and in enhancing additional prevention efforts.
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Robineau O, Frange P, Barin F, Cazein F, Girard PM, Chaix ML, Kreplak G, Boelle PY, Morand-Joubert L. Combining the Estimated Date of HIV Infection with a Phylogenetic Cluster Study to Better Understand HIV Spread: Application in a Paris Neighbourhood. PLoS One 2015; 10:e0135367. [PMID: 26267615 PMCID: PMC4534393 DOI: 10.1371/journal.pone.0135367] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Accepted: 07/21/2015] [Indexed: 11/19/2022] Open
Abstract
Objectives To relate socio-demographic and virological information to phylogenetic clustering in HIV infected patients in a limited geographical area and to evaluate the role of recently infected individuals in the spread of HIV. Methods HIV-1 pol sequences from newly diagnosed and treatment-naive patients receiving follow-up between 2008 and 2011 by physicians belonging to a health network in Paris were used to build a phylogenetic tree using neighbour-joining analysis. Time since infection was estimated by immunoassay to define recently infected patients (very early infected presenters, VEP). Data on socio-demographic, clinical and biological features in clustered and non-clustered patients were compared. Chains of infection structure was also analysed. Results 547 patients were included, 49 chains of infection containing 108 (20%) patients were identified by phylogenetic analysis. analysis. Eighty individuals formed pairs and 28 individuals were belonging to larger clusters. The median time between two successive HIV diagnoses in the same chain of infection was 248 days [CI = 176–320]. 34.7% of individuals were considered as VEP, and 27% of them were included in chains of infection. Multivariable analysis showed that belonging to a cluster was more frequent in VEP and those under 30 years old (OR: 3.65, 95 CI 1.49–8.95, p = 0.005 and OR: 2.42, 95% CI 1.05–5.85, p = 0.04 respectively). The prevalence of drug resistance was not associated with belonging to a pair or a cluster. Within chains, VEP were not grouped together more than chance predicted (p = 0.97). Conclusions Most newly diagnosed patients did not belong to a chain of infection, confirming the importance of undiagnosed or untreated HIV infected individuals in transmission. Furthermore, clusters involving both recently infected individuals and longstanding infected individuals support a substantial role in transmission of the latter before diagnosis.
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Affiliation(s)
- Olivier Robineau
- Service Universitaire Régional de Maladies Infectieuses et Tropicales, Centre Hospitalier de Tourcoing, Tourcoing, France
- INSERM, UMR_S 1136, Institut Pierre Louis d’Epidémiologie et de Santé Publique, Paris, France
- * E-mail: (OR); (LMJ)
| | - Pierre Frange
- EA 3620, Université Paris Descartes, Sorbonne Paris-Cité, Paris, France
- Laboratoire de Microbiologie & Unité d’Immunologie, Hématologie et Rhumatologie Pédiatriques, AP-HP, Hôpital Necker, Enfants Malades, Paris, France
| | - Francis Barin
- Centre National de Référence du VIH & INSERM U966, CHU Bretonneau & Université Francois Rabelais, Tours, France
| | | | - Pierre-Marie Girard
- INSERM, UMR_S 1136, Institut Pierre Louis d’Epidémiologie et de Santé Publique, Paris, France
- Service des Maladies Infectieuses et Tropicales, Hôpital Saint Antoine, APHP, Paris, France
| | - Marie-Laure Chaix
- EA 3620, Université Paris Descartes, Sorbonne Paris-Cité, Paris, France
- Laboratoire de Virologie, AP-HP, Hôpital Saint-Louis, Paris, France
| | | | - Pierre-Yves Boelle
- INSERM, UMR_S 1136, Institut Pierre Louis d’Epidémiologie et de Santé Publique, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 943, Paris, France
- Service de Santé Publique, AP-HP, Hôpital Saint-Antoine, Paris, France
| | - Laurence Morand-Joubert
- INSERM, UMR_S 943, Paris, France
- Laboratoire de Virologie, Hôpital Saint-Antoine, AP-HP, Paris, France
- * E-mail: (OR); (LMJ)
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Zhang J, Shen ZY, Li Z, Liang SJ, He C, Liang FX, Feng Y, Li JJ, Ruan YH, Zhou YJ, Shao YM, Xing H, Liao LJ. Genetic Characteristics of CRF01_AE Among Newly Diagnosed HIV-1-Infected 16- to 25-Year Olds in 3 Geographic Regions of Guangxi, China. Medicine (Baltimore) 2015; 94:e894. [PMID: 26020400 PMCID: PMC4616409 DOI: 10.1097/md.0000000000000894] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The aim of this study was to analyze the distribution of clusters and drug resistance of CRF01_AE among newly diagnosed, treatment-naïve HIV-infected teenagers and young adults in 3 major HIV-affected geographic regions of Guangxi Province, including the cities of Hezhou, Liuzhou, and Nanning. Samples were sequentially collected from newly diagnosed HIV-infected 16- to 25-year olds in these 3 regions from 2009 to 2013. The viral genome was extracted, and the partial pol gene was amplified and sequenced. Phylogenetic analyses were used to determine HIV-1 subtypes and CRF01_AE clusters. Transmitted drug resistance (TDR) mutations were identified using the 2009 WHO list of TDR mutations. A total of 216 sequences were obtained from CRF01_AE strains, which accounted for 83.1% of the 260 genotyped samples, of which 36 were from Hezhou, 147 from Liuzhou, and 33 in Nanning. Most (83.3%, 180/216) were from heterosexuals, followed by injection drug users (5.6%), homosexuals (4.2%), and unknown risk group (6.9%). Based on phylogenetic analyses by the maximum likelihood method, 5 distinct clusters (cluster 1-5) were identified with 213 (98.6%) sequences, whereas 3 (1.4%) sequences were ungrouped. In Hezhou, 88.9% (32/36) of CRF01_AE infections were caused by cluster 2, and 11.1% (4/36) were caused by cluster 1. In Liuzhou, 83.0% (122/147) of the CRF01_AE strains were found in cluster 1, 11.6% (17/147) from cluster 2, 1.4% (2/147) from cluster 3, 2.7% (4/147) from cluster 4, and 0.7% (1/147) from cluster 5. The distribution of CRF01_AE clusters was more even in Nanning than it was in the other 2 regions, with 18.2% (6/33) from cluster 1, 36.3% (12/33) from cluster 2, 9.1% (3/33) from cluster 3, 18.2% (6/33) from cluster 4, and 12.1% (4/33) from cluster 5. The most frequent TDR mutations were M46I (2) in the protease region and Y181C (2) from the reverse transcriptase fragment. Clusters 1 and 2 of CRF01_AE strains were prevalent in Liuzhou and Hezhou, respectively. However, multiple CRF01_AE clusters existed in Nanning. This can be partially explained by the high mobility of laborers in Nanning, the capital city of Guangxi. The prevalence of TDR was low.
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Affiliation(s)
- Jing Zhang
- From the State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing (JZ, ZL, CH, YF, Y-HR, Y-MS, HX, L-JL); and Guangxi Center for Disease Prevention and Control, Nanning, Guangxi Province, China(Z-YS, S-JL, F-XL, J-JL, Y-JZ)
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The rising trend of sexually transmitted infections among HIV-infected persons: a population-based cohort study in Taiwan, 2000 through 2010. J Acquir Immune Defic Syndr 2015; 68:432-8. [PMID: 25501610 DOI: 10.1097/qai.0000000000000477] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Positive prevention interventions for patients living with the HIV include the early detection and treatment of sexually transmitted infections (STIs). This study aimed to determine the incidence of selected STIs, including syphilis, genital warts, gonorrhea, chlamydial infection, and trichomoniasis, in a population-based cohort of individuals living with HIV. METHODS Clinical data from 2000 to 2010 were obtained from the Taiwan National Health Insurance Research Database identified 15,123 patients with HIV infection. The incidence rates were standardized by age and sex using the direct method that was based on the 2000 World Health Organization world standard population. RESULTS The overall rate ratio of STI episodes significantly increased [rate ratio: 34.0, 95% confidence interval (CI): 24.3 to 47.6, P < 0.01]. After an HIV diagnosis, 15.9% of patients with HIV had at least 1 of these 5 STIs. An incidence rate of 503.0 STI episodes/10,000 person-years (PYs) (95% CI: 487.1 to 519.5) was detected during the 11-year follow-up period. The most common STIs after an HIV diagnosis were syphilis (381.9 episodes/10,000 PYs; 95% CI: 368.0 to 396.3), followed by genital warts (138.9 episodes/10,000 PYs; 95% CI: 130.6 to 147.6). The incidence of STIs varied significantly according to gender. In women, the annual incidence of STIs remained stable. However, the annual incidence of syphilis, genital warts, and chlamydial infection increased in young men. CONCLUSIONS An increase in STIs among HIV-positive persons highlights the need to identify the causal factors of these co-infections. Routine STI screenings and early preventive interventions against STIs in HIV-infected persons are crucial.
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Incident sexually transmitted infection as a biomarker for high-risk sexual behavior after diagnosis of acute HIV. Sex Transm Dis 2015; 41:447-52. [PMID: 24922104 DOI: 10.1097/olq.0000000000000147] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND Sexually transmitted infection (STI) diagnosis after diagnosis of acute HIV infection (AHI) indicates ongoing high-risk sexual behavior and possible risk of HIV transmission. We assessed predictors of STI acquisition and the effect of time since care entry on STI incidence in patients with AHI in care and receiving consistent risk-reduction messaging. METHODS Data on incident gonorrhea, chlamydia, trichomoniasis, primary/secondary syphilis, demographic, and clinical risk factors were abstracted from medical charts for patients diagnosed as having AHI and engaged in care. Poisson regression models using generalized estimating equations were fit to estimate incidence rates (IRs), IR ratios, and robust 95% confidence intervals. RESULTS Among 185 patients with AHI, 26 (14%) were diagnosed as having at least 1 incident STI over 709.4 person-years; 46 STIs were diagnosed during follow-up (IR, 6.8/100 person-years). The median time from HIV care entry to first STI diagnosis was 609 days (range, 168-1681 days). Men who have sex with men (P = 0.03), a shorter time between presentation to medical care and AHI diagnosis (P = 0.06), and STI diagnosis before AHI diagnosis (P = 0.0003) were predictors of incident STI. Sexually transmitted infection IR greater than 1 year after entering care was double that of patients in care 1 year or less (IR ratio, 2.0; 95% confidence interval, 0.8-4.9). HIV viral load was above the limits of detection within 1 month of 11 STI diagnoses in 6 patients (23.1%) (median, 15,898 copies/mL; range, 244-152,000 copies/mL). CONCLUSIONS Despite regular HIV care, STI incidence was high among this primarily young, men who have sex with men AHI cohort. Early antiretroviral initiation may decrease HIV transmission given ongoing risk behaviors despite risk-reduction messaging.
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Transmission clustering among newly diagnosed HIV patients in Chicago, 2008 to 2011: using phylogenetics to expand knowledge of regional HIV transmission patterns. J Acquir Immune Defic Syndr 2015; 68:46-54. [PMID: 25321182 DOI: 10.1097/qai.0000000000000404] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION HIV transmission cluster analyses can inform HIV prevention efforts. We describe the first such assessment for transmission clustering among HIV patients in Chicago. METHODS We performed transmission cluster analyses using HIV pol sequences from newly diagnosed patients presenting to Chicago's largest HIV clinic between 2008 and 2011. We compared sequences through progressive pairwise alignment, using neighbor joining to construct an unrooted phylogenetic tree. We defined clusters as >2 sequences among which each sequence had at least 1 partner within a genetic distance of ≤1.5%. We used multivariable regression to examine factors associated with clustering and used geospatial analysis to assess geographic proximity of phylogenetically clustered patients. RESULTS We compared sequences from 920 patients, median age of 35 years, 75% male, 67% black, 23% Hispanic, and 8% had a rapid plasma reagin titer ≥1:16 concurrent with their HIV diagnosis. We had HIV transmission risk data for 54%; 43% identified as men who have sex with men (MSM). Phylogenetic analysis demonstrated 123 patients (13%) grouped into 26 clusters, the largest having 20 members. In multivariable regression, age <25, black race, MSM status, male gender, higher HIV viral load, and rapid plasma reagin ≥1:16 associated with clustering. We did not observe geographic grouping of genetically clustered patients. DISCUSSION Our results demonstrate high rates of HIV transmission clustering, without local geographic foci, among young black MSM in Chicago. Applied prospectively, phylogenetic analyses could guide prevention efforts and help break the cycle of transmission.
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Mandating the offer of HIV testing in New York: simulating the epidemic impact and resource needs. J Acquir Immune Defic Syndr 2015; 68 Suppl 1:S59-67. [PMID: 25545496 DOI: 10.1097/qai.0000000000000395] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND A 2010 New York law requires that patients aged 13-64 years be offered HIV testing in routine medical care settings. Past studies report the clinical outcomes, cost-effectiveness, and budget impact of expanded HIV testing nationally and within clinics but have not examined how state policies affect resource needs and epidemic outcomes. METHODS A system dynamics model of HIV testing and care was developed, where disease progression and transmission differ by awareness of HIV status, engagement in care, and disease stage. Data sources include HIV surveillance, Medicaid claims, and literature. The model projected how alternate implementation scenarios would change new infections, diagnoses, linkage to care, and living HIV cases over 10 years. RESULTS Without the law, the model projects declining new infections, newly diagnosed cases, individuals newly linked to care, and fraction of undiagnosed cases (reductions of 62.8%, 59.7%, 54.1%, and 57.8%) and a slight increase in living diagnosed cases and individuals in care (2.2% and 6.1%). The law will further reduce new infections, diagnosed AIDS cases, and the fraction undiagnosed and initially increase and then decrease newly diagnosed cases. Outcomes were consistent across scenarios with different testing offer frequencies and implementation times but differed according to the level of implementation. CONCLUSIONS A mandatory offer of HIV testing may increase diagnoses and avert infections but will not eliminate the epidemic. Despite declines in new infections, previously diagnosed cases will continue to need access to antiretroviral therapy, highlighting the importance of continued funding for HIV care.
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Frost SDW, Pillay D. Understanding drivers of phylogenetic clustering in molecular epidemiological studies of HIV. J Infect Dis 2014; 211:856-8. [PMID: 25312038 PMCID: PMC4340367 DOI: 10.1093/infdis/jiu563] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Simon D W Frost
- Department of Veterinary Medicine and Institute of Public Health, University of Cambridge
| | - Deenan Pillay
- University College London, United Kingdom Africa Centre for Health and Population Studies, University of KwaZulu Natal, Durban, South Africa
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Dennis AM, Herbeck JT, Brown AL, Kellam P, de Oliveira T, Pillay D, Fraser C, Cohen MS. Phylogenetic studies of transmission dynamics in generalized HIV epidemics: an essential tool where the burden is greatest? J Acquir Immune Defic Syndr 2014; 67:181-95. [PMID: 24977473 PMCID: PMC4304655 DOI: 10.1097/qai.0000000000000271] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Efficient and effective HIV prevention measures for generalized epidemics in sub-Saharan Africa have not yet been validated at the population level. Design and impact evaluation of such measures requires fine-scale understanding of local HIV transmission dynamics. The novel tools of HIV phylogenetics and molecular epidemiology may elucidate these transmission dynamics. Such methods have been incorporated into studies of concentrated HIV epidemics to identify proximate and determinant traits associated with ongoing transmission. However, applying similar phylogenetic analyses to generalized epidemics, including the design and evaluation of prevention trials, presents additional challenges. Here we review the scope of these methods and present examples of their use in concentrated epidemics in the context of prevention. Next, we describe the current uses for phylogenetics in generalized epidemics and discuss their promise for elucidating transmission patterns and informing prevention trials. Finally, we review logistic and technical challenges inherent to large-scale molecular epidemiological studies of generalized epidemics and suggest potential solutions.
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Affiliation(s)
- Ann M. Dennis
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Andrew Leigh Brown
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Cambridge, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Tulio de Oliveira
- Wellcome Trust-Africa Centre for Health and Population Studies, University of Kwazula-Natal, ZA
| | - Deenan Pillay
- Division of Infection and Immunity, University College London, London, UK
| | - Christophe Fraser
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Myron S. Cohen
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC
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Impact of viral load and the duration of primary infection on HIV transmission: systematic review and meta-analysis. AIDS 2014; 28:1021-9. [PMID: 24691205 DOI: 10.1097/qad.0000000000000135] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
OBJECTIVES HIV 'treatment as prevention' (TasP) describes early treatment of HIV-infected patients intended to reduce viral load and transmission. Crucial assumptions for estimating TasP's effectiveness are the underlying estimates of transmission risk. We aimed to determine transmission risk during primary infection, and describe the relation of HIV transmission risk to viral load. DESIGN A systematic review and meta-analysis. METHODS We searched PubMed and Embase databases for studies that established a relationship between viral load and transmission risk, or primary infection and transmission risk, in serodiscordant couples. We analysed assumptions about the relationship between viral load and transmission risk, and between duration of primary infection and transmission risk. RESULTS We found 36 eligible articles, based on six different study populations. Studies consistently found that higher viral loads lead to higher HIV transmission rates, but assumptions about the shape of this increase varied from exponential increase to saturation. The assumed duration of primary infection ranged from 1.5 to 12 months; for each additional month, the log10 transmission rate ratio between primary and asymptomatic infection decreased by 0.40. CONCLUSION Assumptions and estimates of the relationship between viral load and transmission risk, and the relationship between primary infection and transmission risk, vary substantially and predictions of TasP's effectiveness should take this uncertainty into account.
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Ross LL, Horton J, Hasan S, Brown JR, Murphy D, DeJesus E, Potter M, LaMarca A, Melendez-Rivera I, Ward D, Uy J, Shaefer MS. HIV-1 transmission patterns in antiretroviral therapy-naïve, HIV-infected North Americans based on phylogenetic analysis by population level and ultra-deep DNA sequencing. PLoS One 2014; 9:e89611. [PMID: 24586911 PMCID: PMC3935917 DOI: 10.1371/journal.pone.0089611] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 01/22/2014] [Indexed: 11/18/2022] Open
Abstract
Factors that contribute to the transmission of human immunodeficiency virus type 1 (HIV-1), especially drug-resistant HIV-1 variants remain a significant public health concern. In-depth phylogenetic analyses of viral sequences obtained in the screening phase from antiretroviral-naïve HIV-infected patients seeking enrollment in EPZ108859, a large open-label study in the USA, Canada and Puerto Rico (ClinicalTrials.gov NCT00440947) were examined for insights into the roles of drug resistance and epidemiological factors that could impact disease dissemination. Viral transmission clusters (VTCs) were initially predicted from a phylogenetic analysis of population level HIV-1 pol sequences obtained from 690 antiretroviral-naïve subjects in 2007. Subsequently, the predicted VTCs were tested for robustness by ultra deep sequencing (UDS) using pyrosequencing technology and further phylogenetic analyses. The demographic characteristics of clustered and non-clustered subjects were then compared. From 690 subjects, 69 were assigned to 1 of 30 VTCs, each containing 2 to 5 subjects. Race composition of VTCs were significantly more likely to be white (72% vs. 60%; p = 0.04). VTCs had fewer reverse transcriptase and major PI resistance mutations (9% vs. 24%; p = 0.002) than non-clustered sequences. Both men-who-have-sex-with-men (MSM) (68% vs. 48%; p = 0.001) and Canadians (29% vs. 14%; p = 0.03) were significantly more frequent in VTCs than non-clustered sequences. Of the 515 subjects who initiated antiretroviral therapy, 33 experienced confirmed virologic failure through 144 weeks while only 3/33 were from VTCs. Fewer VTCs subjects (as compared to those with non-clustering virus) had HIV-1 with resistance-associated mutations or experienced virologic failure during the course of the study. Our analysis shows specific geographical and drug resistance trends that correlate well with transmission clusters defined by HIV sequences of similarity. Furthermore, our study demonstrates the utility of molecular and epidemiological analysis of VTCs for identifying population-specific risks associated with HIV-1 transmission and developing effective local healthcare strategies.
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Affiliation(s)
- Lisa L. Ross
- ViiV HealthCare, Research Triangle Park, North Carolina, United States of America
- * E-mail:
| | - Joseph Horton
- GlaxoSmithKline, Research Triangle Park, North Carolina, United States of America
| | | | - James R. Brown
- GlaxoSmithKline, Research Triangle Park, North Carolina, United States of America
| | | | - Edwin DeJesus
- Orlando Immunology Center, Orlando, Florida, United States of America
| | - Martin Potter
- McGill University Health Centre, Montreal, QC, Canada
| | - Anthony LaMarca
- Therafirst Medical Center, Ft Lauderdale, Florida, United States of America
| | | | - Douglas Ward
- Dupont Circle Physicians Group, Washington, DC, United States of America
| | - Jonathon Uy
- Amicus Therapeutics, Cranbury, New Jersey, United States of America
| | - Mark S. Shaefer
- ViiV HealthCare, Research Triangle Park, North Carolina, United States of America
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40
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4.0 When to start. HIV Med 2013. [DOI: 10.1111/hiv.12119_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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HIV-1 transmission during early infection in men who have sex with men: a phylodynamic analysis. PLoS Med 2013; 10:e1001568; discussion e1001568. [PMID: 24339751 PMCID: PMC3858227 DOI: 10.1371/journal.pmed.1001568] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 10/23/2013] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Conventional epidemiological surveillance of infectious diseases is focused on characterization of incident infections and estimation of the number of prevalent infections. Advances in methods for the analysis of the population-level genetic variation of viruses can potentially provide information about donors, not just recipients, of infection. Genetic sequences from many viruses are increasingly abundant, especially HIV, which is routinely sequenced for surveillance of drug resistance mutations. We conducted a phylodynamic analysis of HIV genetic sequence data and surveillance data from a US population of men who have sex with men (MSM) and estimated incidence and transmission rates by stage of infection. METHODS AND FINDINGS We analyzed 662 HIV-1 subtype B sequences collected between October 14, 2004, and February 24, 2012, from MSM in the Detroit metropolitan area, Michigan. These sequences were cross-referenced with a database of 30,200 patients diagnosed with HIV infection in the state of Michigan, which includes clinical information that is informative about the recency of infection at the time of diagnosis. These data were analyzed using recently developed population genetic methods that have enabled the estimation of transmission rates from the population-level genetic diversity of the virus. We found that genetic data are highly informative about HIV donors in ways that standard surveillance data are not. Genetic data are especially informative about the stage of infection of donors at the point of transmission. We estimate that 44.7% (95% CI, 42.2%-46.4%) of transmissions occur during the first year of infection. CONCLUSIONS In this study, almost half of transmissions occurred within the first year of HIV infection in MSM. Our conclusions may be sensitive to un-modeled intra-host evolutionary dynamics, un-modeled sexual risk behavior, and uncertainty in the stage of infected hosts at the time of sampling. The intensity of transmission during early infection may have significance for public health interventions based on early treatment of newly diagnosed individuals.
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Cambiano V, O'Connor J, Phillips AN, Rodger A, Lodwick R, Pharris A, Lampe F, Nakagawa F, Smith C, van de Laar MJ. Antiretroviral therapy for prevention of HIV transmission: implications for Europe. ACTA ACUST UNITED AC 2013; 18:20647. [PMID: 24308982 DOI: 10.2807/1560-7917.es2013.18.48.20647] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The aim of this review is to summarise the evidence on the population-level effect of antiretroviral therapy (ART) in preventing HIV infections, and to discuss potential implications in the European context of recommending starting ART when the CD4 count is above 350 cells/mm3. The ability of ART to reduce the risk of HIV transmission has been reported in observational studies and in a randomised controlled trial (HPTN 052), in which ART initiation reduced HIV transmission by 96% within serodiscordant couples. As yet, there is no direct evidence for such an effect among men having sex with men or people who inject drugs. HPTN 052 led international organisations to develop recommendations with a higher CD4 threshold for ART initiation. However, there remains a lack of strong evidence of clinical benefit for HIV-positive individuals starting ART with CD4 count above 350 cells/mm3. The main goal of ART provision should be to increase ART coverage for all those in need, based on the current guidelines, and the offer of ART to those who wish to reduce infectivity; increased HIV testing is therefore a key requirement. Other proven prevention means such as condom use and harm reduction for people who inject drugs remain critical.
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Affiliation(s)
- V Cambiano
- Research Department of Infection and Population Health, Institute of Epidemiology and Health Care, University College London, London, United Kingdom
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43
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Ragonnet-Cronin M, Hodcroft E, Hué S, Fearnhill E, Delpech V, Brown AJL, Lycett S. Automated analysis of phylogenetic clusters. BMC Bioinformatics 2013; 14:317. [PMID: 24191891 PMCID: PMC4228337 DOI: 10.1186/1471-2105-14-317] [Citation(s) in RCA: 251] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 10/30/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND As sequence data sets used for the investigation of pathogen transmission patterns increase in size, automated tools and standardized methods for cluster analysis have become necessary. We have developed an automated Cluster Picker which identifies monophyletic clades meeting user-input criteria for bootstrap support and maximum genetic distance within large phylogenetic trees. A second tool, the Cluster Matcher, automates the process of linking genetic data to epidemiological or clinical data, and matches clusters between runs of the Cluster Picker. RESULTS We explore the effect of different bootstrap and genetic distance thresholds on clusters identified in a data set of publicly available HIV sequences, and compare these results to those of a previously published tool for cluster identification. To demonstrate their utility, we then use the Cluster Picker and Cluster Matcher together to investigate how clusters in the data set changed over time. We find that clusters containing sequences from more than one UK location at the first time point (multiple origin) were significantly more likely to grow than those representing only a single location. CONCLUSIONS The Cluster Picker and Cluster Matcher can rapidly process phylogenetic trees containing tens of thousands of sequences. Together these tools will facilitate comparisons of pathogen transmission dynamics between studies and countries.
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Abstract
The success of the HIV Prevention Trials Network 052 trial has led to revisions in HIV-1 treatment guidelines. Antiretroviral therapy may reduce the risk of HIV-1 transmissions at the population level. The design of successful treatment as prevention interventions will be predicated on a comprehensive understanding of the spatial, temporal, and biological dynamics of heterosexual men who have sex with men and intravenous drug user epidemics. Viral phylogenetics can capture the underlying structure of transmission networks based on the genetic interrelatedness of viral sequences and cluster networks that could not be otherwise identified. This article describes the phylogenetic expansion of the Montreal men who have sex with men epidemic over the last decade. High rates of coclustering of primary infections are associated with 1 infection leading to 13 onward transmissions. Phylogeny substantiates the role of primary and recent stage infection in transmission dynamics, underlying the importance of timely diagnosis and immediate antiretroviral therapy initiation to avert transmission cascades.
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Affiliation(s)
- Bluma G Brenner
- Lady Davis Research Institute, Jewish General Hospital, McGill AIDS Centre, McGill University, Montreal, Canada
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45
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Smith MK, Rutstein SE, Powers KA, Fidler S, Miller WC, Eron JJ, Cohen MS. The detection and management of early HIV infection: a clinical and public health emergency. J Acquir Immune Defic Syndr 2013; 63 Suppl 2:S187-99. [PMID: 23764635 PMCID: PMC4015137 DOI: 10.1097/qai.0b013e31829871e0] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
This review considers the detection and management of early HIV infection (EHI), defined here as the first 6 months of infection. This phase is clinically important because a reservoir of infected cells formed in the individual renders HIV incurable, and the magnitude of viremia at the end of this period predicts the natural history of disease. Epidemiologically, it is critical because the very high viral load that typically accompanies early infection also makes infected individuals maximally contagious to their sexual partners. Future efforts to prevent HIV transmission with expanded testing and treatment may be compromised by elevated transmission risk earlier in the course of HIV infection, although the extent of this impact is yet unknown. Treatment as prevention efforts will nevertheless need to develop strategies to address testing, linkage to care, and treatment of EHI. Cost-effective and efficient identification of more persons with early HIV will depend on advancements in diagnostic technology and strengthened symptom-based screening strategies. Treatment for persons with EHI must balance individual health benefits and reduction of the risk of onward viral transmission. An increasing body of evidence supports the use of immediate antiretroviral therapy to treat EHI to maintain CD4 count and functionality, limit the size of the HIV reservoir, and reduce the risk of onward viral transmission. Although we can anticipate considerable challenges in identifying and linking to care persons in the earliest phases of HIV infection, there are many reasons to pursue this strategy.
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Affiliation(s)
- M Kumi Smith
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Hightower GK, May SJ, Pérez-Santiago J, Pacold ME, Wagner GA, Little SJ, Richman DD, Mehta SR, Smith DM, Pond SLK. HIV-1 clade B pol evolution following primary infection. PLoS One 2013; 8:e68188. [PMID: 23840830 PMCID: PMC3695957 DOI: 10.1371/journal.pone.0068188] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 05/27/2013] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE Characterize intra-individual HIV-1 subtype B pol evolution in antiretroviral naive individuals. DESIGN Longitudinal cohort study of individuals enrolled during primary infection. METHODS Eligible individuals were antiretroviral naïve participants enrolled in the cohort from December 1997-December 2005 and having at least two blood samples available with the first one collected within a year of their estimated date of infection. Population-based pol sequences were generated from collected blood samples and analyzed for genetic divergence over time in respect to dual infection status, HLA, CD4 count and viral load. RESULTS 93 participants were observed for a median of 1.8 years (Mean = 2.2 years, SD =1.9 years). All participants classified as mono-infected had less than 0.7% divergence between any two of their pol sequences using the Tamura-Nei model (TN93), while individuals with dual infection had up to 7.0% divergence. The global substitution rates (substitutions/nucleotide/year) for mono and dually infected individuals were significantly different (p<0.001); however, substitution rates were not associated with HLA haplotype, CD4 or viral load. CONCLUSIONS Even after a maximum of almost 9 years of follow-up, all mono-infected participants had less than 1% divergence between baseline and longitudinal sequences, while participants with dual infection had 10 times greater divergence. These data support the use of HIV-1 pol sequence data to evaluate transmission events, networks and HIV-1 dual infection.
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Affiliation(s)
- George K. Hightower
- Department of Medicine, University of California San Diego, La Jolla, California United States of America
| | - Susanne J. May
- Department of Biostatistics, University of Washington, Seattle, Washington United States of America
| | - Josué Pérez-Santiago
- Department of Medicine, University of California San Diego, La Jolla, California United States of America
| | - Mary E. Pacold
- Life Technologies, San Francisco, California United States of America
| | - Gabriel A. Wagner
- Department of Medicine, University of California San Diego, La Jolla, California United States of America
| | - Susan J. Little
- Department of Medicine, University of California San Diego, La Jolla, California United States of America
| | - Douglas D. Richman
- Department of Medicine, University of California San Diego, La Jolla, California United States of America
- Veterans Administration San Diego Healthcare System, San Diego, California, United States of America
| | - Sanjay R. Mehta
- Department of Medicine, University of California San Diego, La Jolla, California United States of America
| | - Davey M. Smith
- Department of Medicine, University of California San Diego, La Jolla, California United States of America
- Veterans Administration San Diego Healthcare System, San Diego, California, United States of America
- * E-mail:
| | - Sergei L. Kosakovsky Pond
- Department of Medicine, University of California San Diego, La Jolla, California United States of America
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Siconolfi DE, Kapadia F, Halkitis PN, Moeller RW, Storholm ED, Barton SC, Solomon TM, Jones D. Sexual health screening among racially/ethnically diverse young gay, bisexual, and other men who have sex with men. J Adolesc Health 2013; 52:620-6. [PMID: 23298989 PMCID: PMC3634893 DOI: 10.1016/j.jadohealth.2012.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 10/02/2012] [Accepted: 10/05/2012] [Indexed: 11/24/2022]
Abstract
PURPOSE Screening for sexually transmitted infections (STIs) is a crucial element of improving health and reducing disparities, and young men who have sex with men (YMSM) face high rates of both STIs and human immunodeficiency virus. We examined sexual health screening among a diverse sample of adolescent YMSM living in New York City. METHODS Between 2009 and 2011, cross-sectional data were collected from 590 YMSM in New York City. Separate multivariable logistic regression models were used to assess the relationship between sociodemographic, psychosocial, and health and healthcare related factors and two main outcomes: having sought a recent sexual health screening (past 6 months) and having a rectal sexual health screening (lifetime). RESULTS Overall, 46% reported a sexual health screening in the prior 6 months, but only 16% reported ever having a rectal screening for STIs. Rates were higher among ethnic minority YMSM and men who accessed care at clinics. Multivariable results indicated that gay community affiliation, recent unprotected anal sex, and number of lifetime male partners were also associated with seeking a recent screening. CONCLUSIONS Though half of the sample reported recent general screening, rates of lifetime rectal screening are low. Efforts to increase screening may focus on improving provider knowledge and guideline adherence, and educating and encouraging YMSM to access sexual health check-ups.
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Affiliation(s)
- Daniel E Siconolfi
- Center for Health, Identity, Behavior & Prevention Studies (CHIBPS), Steinhardt School of Culture, Education & Human Development, New York University, New York, NY, USA.
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Phylogenetic inferences on HIV-1 transmission: implications for the design of prevention and treatment interventions. AIDS 2013; 27:1045-57. [PMID: 23902920 DOI: 10.1097/qad.0b013e32835cffd9] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Smoleń-Dzirba J, Rosińska M, Kruszyński P, Bratosiewicz-Wąsik J, Janiec J, Beniowski M, Bociąga-Jasik M, Jabłonowska E, Szetela B, Porter K, Wąsik TJ. Molecular epidemiology of recent HIV-1 infections in southern Poland. J Med Virol 2013; 84:1857-68. [PMID: 23080488 DOI: 10.1002/jmv.23395] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The genetic diversity of human immunodeficiency virus type 1 (HIV-1) offers an opportunity to track the development of the epidemic across different populations. Viral pol gene fragments from 55 individuals of Polish origin with recent HIV-1 infection identified in 2008-2010 in four Polish cities were analyzed. Viral sequences were compared with sequences from 100 individuals (reference group) infected before 2004. Viral spread among groups with different HIV transmission categories was compared using a phylogenetic approach. The majority of sequences from individuals with recent infection were subtype B (93%) within which four transmission clusters (18% of samples) were detected. Samples from men infected through sex between men and from persons infected through injecting drugs were broadly separated (P < 0.0001), while samples from individuals infected by heterosexual contacts were dispersed uniformly within phylogenetic tree (P = 0.244) inferred from viral sequences derived from individuals infected recently and the reference group. The percentage of samples from persons infected by heterosexual contacts which clustered with samples from men infected through sex between men was not significantly higher for those with recent infection (47%), compared to the reference group (36%). In conclusion, men infected by sex between men and individuals infected through injecting drugs appear to form separate HIV transmission networks in Poland. The recent spread of HIV-1 among persons infected with subtype B by heterosexual contacts appears to be linked to both these groups.
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Affiliation(s)
- Joanna Smoleń-Dzirba
- Department and Institute of Microbiology and Virology, The School of Pharmacy and Division of Laboratory Medicine, Medical University of Silesia, Katowice, Poland
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Yebra G, Holguín Á, Pillay D, Hué S. Phylogenetic and demographic characterization of HIV-1 transmission in Madrid, Spain. INFECTION GENETICS AND EVOLUTION 2013; 14:232-9. [DOI: 10.1016/j.meegid.2012.12.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 12/10/2012] [Accepted: 12/12/2012] [Indexed: 11/26/2022]
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