1
|
Planinić A, Begovac J, Rokić F, Šimičić P, Oroz M, Jakovac K, Vugrek O, Zidovec-Lepej S. Characterization of Human Immunodeficiency Virus-1 Transmission Clusters and Transmitted Drug-Resistant Mutations in Croatia from 2019 to 2022. Viruses 2023; 15:2408. [PMID: 38140649 PMCID: PMC10747707 DOI: 10.3390/v15122408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/04/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Molecular epidemiology of HIV-1 infection is challenging due to the highly diverse HIV-genome. We investigated the genetic diversity and prevalence of transmitted drug resistance (TDR) followed by phylogenetic analysis in 270 HIV-1 infected, treatment-naïve individuals from Croatia in the period 2019-2022. The results of this research confirmed a high overall prevalence of TDR of 16.7%. Resistance to nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside RTIs (NNRTIs), and protease inhibitors (PIs) was found in 9.6%, 7.4%, and 1.5% of persons, respectively. No resistance to integrase strand-transfer inhibitors (INSTIs) was found. Phylogenetic analysis revealed that 173/229 sequences (75.5%) were part of transmission clusters, and the largest identified was T215S, consisting of 45 sequences. Forward transmission was confirmed in several clusters. We compared deep sequencing (DS) with Sanger sequencing (SS) on 60 randomly selected samples and identified additional surveillance drug resistance mutations (SDRMs) in 49 of them. Our data highlight the need for baseline resistance testing in treatment-naïve persons. Although no major INSTIs were found, monitoring of SDRMs to INSTIs should be continued due to the extensive use of first- and second-generation INSTIs.
Collapse
Affiliation(s)
- Ana Planinić
- Department of Immunological and Molecular Diagnostics, University Hospital for Infectious Diseases Dr. Fran Mihaljević, 10000 Zagreb, Croatia;
| | - Josip Begovac
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
| | - Filip Rokić
- Ruđer Bošković Institute, 10000 Zagreb, Croatia; (F.R.); (K.J.); (O.V.)
| | - Petra Šimičić
- Department of Oncology and Nuclear Medicine, Sestre Milosrdnice University Hospital Center, 10000 Zagreb, Croatia;
| | - Maja Oroz
- Cytogenetic Laboratory, Department of Obstetrics and Gynecology, Clinical Hospital Sveti Duh, 10000 Zagreb, Croatia;
| | - Katja Jakovac
- Ruđer Bošković Institute, 10000 Zagreb, Croatia; (F.R.); (K.J.); (O.V.)
| | - Oliver Vugrek
- Ruđer Bošković Institute, 10000 Zagreb, Croatia; (F.R.); (K.J.); (O.V.)
| | - Snjezana Zidovec-Lepej
- Department of Immunological and Molecular Diagnostics, University Hospital for Infectious Diseases Dr. Fran Mihaljević, 10000 Zagreb, Croatia;
| |
Collapse
|
2
|
Viñuela L, de Salazar A, Fuentes A, Serrano-Conde E, Falces-Romero I, Pinto A, Portilla I, Masiá M, Peraire J, Gómez-Sirvent JL, Sanchiz M, Iborra A, Baza B, Aguilera A, Olalla J, Espinosa N, Iribarren JA, Martínez-Velasco M, Imaz A, Montero M, Rivero M, Suarez-García I, Maciá MD, Galán JC, Perez-Elias MJ, García-Fraile LJ, Moreno C, Garcia F. Transmitted drug resistance to antiretroviral drugs in Spain during the period 2019-2021. J Med Virol 2023; 95:e29287. [PMID: 38084763 DOI: 10.1002/jmv.29287] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 10/17/2023] [Accepted: 11/18/2023] [Indexed: 12/18/2023]
Abstract
To evaluate the prevalence of transmitted drug resistance (TDR) to nucleoside and nonnucleoside reverse transcriptase inhibitors (NRTI, NNRTI), protease inhibitors (PI), and integrase strand transfer inhibitors (INSTI) in Spain during the period 2019-2021, as well as to evaluate transmitted clinically relevant resistance (TCRR) to antiretroviral drugs. Reverse transcriptase (RT), protease (Pro), and Integrase (IN) sequences from 1824 PLWH (people living with HIV) were studied. To evaluate TDR we investigated the prevalence of surveillance drug resistance mutations (SDRM). To evaluate TCRR (any resistance level ≥ 3), and for HIV subtyping we used the Stanford v.9.4.1 HIVDB Algorithm and an in-depth phylogenetic analysis. The prevalence of NRTI SDRMs was 3.8% (95% CI, 2.8%-4.6%), 6.1% (95% CI, 5.0%-7.3%) for NNRTI, 0.9% (95% CI, 0.5%-1.4%) for PI, and 0.2% (95% CI, 0.0%-0.9%) for INSTI. The prevalence of TCRR to NRTI was 2.1% (95% CI, 1.5%-2.9%), 11.8% for NNRTI, (95% CI, 10.3%-13.5%), 0.2% (95% CI, 0.1%-0.6%) for PI, and 2.5% (95% CI, 1.5%-4.1%) for INSTI. Most of the patients were infected by subtype B (79.8%), while the majority of non-Bs were CRF02_AG (n = 109, 6%). The prevalence of INSTI and PI resistance in Spain during the period 2019-2021 is low, while NRTI resistance is moderate, and NNRTI resistance is the highest. Our results support the use of integrase inhibitors as first-line treatment in Spain. Our findings highlight the importance of ongoing surveillance of TDR to antiretroviral drugs in PLWH particularly with regard to first-line antiretroviral therapy.
Collapse
Affiliation(s)
- Laura Viñuela
- Clinical Microbiology Unit, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Ibs, Granada, Spain
- Ciber de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
| | - Adolfo de Salazar
- Clinical Microbiology Unit, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Ibs, Granada, Spain
- Ciber de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
| | - Ana Fuentes
- Clinical Microbiology Unit, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Ibs, Granada, Spain
- Ciber de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
| | - Esther Serrano-Conde
- Clinical Microbiology Unit, Hospital Universitario Clínico San Cecilio, Granada, Spain
| | | | - Adriana Pinto
- Infectious Diseases Unit, Hospital 12 de Octubre, Madrid, Spain
| | - Irene Portilla
- Infectious Diseases Unit, Hospital General Universitario de Alicante, Alicante, Spain
| | - Mar Masiá
- Ciber de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
- Infectious Diseases Unit, Hospital General Universitario de Elche, Elche, Spain
| | - Joaquim Peraire
- Ciber de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
- Infectious Diseases Unit, Hospital Universitari de Tarragona Joan XXIII, IISPV, Universitat Rovira i Virgili, Tarragona, Spain
| | - Juan Luis Gómez-Sirvent
- Infectious Diseases Unit, Hospital Universitario de Canarias, Las Palmas de Gran Canaria, Spain
| | - Marta Sanchiz
- Infectious Diseases Unit, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Asunción Iborra
- Clinical Microbiology Unit, Hospital Virgen de la Arrixaca, Murcia, Spain
| | - Begoña Baza
- Centro Sanitario Sandoval, Hospital Clínico San Carlos, Madrid, Spain
- Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
- Instituto de Medicina de Laboratorio (IML), Madrid, Spain
| | - Antonio Aguilera
- Clinical Microbiology Unit, Complejo Hospitalario Universitario de Santiago, Santiago, Spain
| | - Julián Olalla
- Infectious Diseases Unit, Hospital Costa del Sol, Marbella, Spain
| | - Nuria Espinosa
- Infectious Diseases Unit, Hospital Virgen del Rocío, Seville, Spain
| | | | | | - Arkaitz Imaz
- Infectious Diseases Unit, Hospital Universitario de Bellvitge, Barcelona, Spain
| | - Marta Montero
- Infectious Diseases Unit, Hospital Universitario La Fe, Valencia, Spain
| | - María Rivero
- Infectious Diseases Unit, Hospital de Navarra, Pamplona, Spain
| | | | | | - Juan Carlos Galán
- Infectious Diseases Unit, Hospital Ramón y Cajal, Madrid, Spain
- Ciber de Epidemiologia y Salud Publica, CIBERESP, Madrid, Spain
- Insituto Ramón y Cajal de Investigación Sanitaria (IRYSCIS), Madrid, Spain
| | - Maria Jesus Perez-Elias
- Ciber de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
- Infectious Diseases Unit, Hospital Ramón y Cajal, Madrid, Spain
| | | | - Cristina Moreno
- Ciber de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
- Instituto de Salud Carlos III, Madrid, Spain
| | - Federico Garcia
- Clinical Microbiology Unit, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Ibs, Granada, Spain
- Ciber de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
| |
Collapse
|
3
|
Maggiorella MT, Sernicola L, Picconi O, Pizzi E, Belli R, Fulgenzi D, Rovetto C, Bruni R, Costantino A, Taffon S, Chionne P, Madonna E, Pisani G, Borsetti A, Falvino C, Ranieri R, Baccalini R, Pansera A, Castelvedere F, Babudieri S, Madeddu G, Starnini G, Dell'Isola S, Cervellini P, Ciccaglione AR, Ensoli B, Buttò S. Epidemiological and molecular characterization of HBV and HCV infections in HIV-1-infected inmate population in Italy: a 2017-2019 multicenter cross-sectional study. Sci Rep 2023; 13:14908. [PMID: 37689795 PMCID: PMC10492787 DOI: 10.1038/s41598-023-41814-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/31/2023] [Indexed: 09/11/2023] Open
Abstract
HBV/HCV co-infection is common in HIV-1-infected prisoners. To investigate the characteristics of HIV co-infections, and to evaluate the molecular heterogeneity of HIV, HBV and HCV in prisoners, we carried-out a multicenter cross-sectional study, including 65 HIV-1-infected inmates enrolled in 5 Italian detention centers during the period 2017-2019. HIV-1 subtyping showed that 77.1% of inmates were infected with B subtype and 22.9% with non-B subtypes. Italian nationals were all infected with subtype B (93.1%), except two individuals, one infected with the recombinant form CRF72_BF1, and the other with the HIV-1 sub-subtype A6, both previously not identified in inmates of Italian nationality. Non-Italian nationals were infected with subtype B (52.6%), CRFs (36.8%) and sub-subtypes A1 and A3 (5.2%). HIV variants carrying resistance mutations to NRTI, NNRTI, PI and InSTI were found in 7 inmates, 4 of which were never exposed to the relevant classes of drugs associated with these mutations. HBV and/or HCV co-infections markers were found in 49/65 (75.4%) inmates, while 27/65 (41.5%) showed markers of both HBV and HCV coinfection. Further, Italian nationals showed a significant higher presence of HCV markers as compared to non-Italian nationals (p = 0.0001). Finally, HCV phylogenetic analysis performed in 18 inmates revealed the presence of HCV subtypes 1a, 3a, 4d (66.6%, 16.7% and 16.7%, respectively). Our data suggest the need to monitor HIV, HBV and HCV infections in prisons in order to prevent spreading of these viruses both in jails and in the general population, and to implement effective public health programs that limit the circulation of different genetic forms as well as of viral variants with mutations conferring resistance to treatment.
Collapse
Affiliation(s)
- Maria Teresa Maggiorella
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, V.le Regina Elena 299, 00161, Rome, Italy.
| | - L Sernicola
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, V.le Regina Elena 299, 00161, Rome, Italy
| | - O Picconi
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, V.le Regina Elena 299, 00161, Rome, Italy
| | - E Pizzi
- Core Facilities, Istituto Superiore di Sanità, Rome, Italy
| | - R Belli
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, V.le Regina Elena 299, 00161, Rome, Italy
| | - D Fulgenzi
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, V.le Regina Elena 299, 00161, Rome, Italy
| | - C Rovetto
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, V.le Regina Elena 299, 00161, Rome, Italy
| | - R Bruni
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - A Costantino
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - S Taffon
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - P Chionne
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - E Madonna
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - G Pisani
- National Center for Immunobiologicals, Research and Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | - A Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, V.le Regina Elena 299, 00161, Rome, Italy
| | - C Falvino
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, V.le Regina Elena 299, 00161, Rome, Italy
| | - R Ranieri
- Infectious Diseases Service, Penitentiary Health System, Azienda Socio-Sanitaria Territoriale Santi Paolo e Carlo, Milan, Italy
| | | | | | | | - S Babudieri
- Infectious Diseases Unit, Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
| | - G Madeddu
- Infectious Diseases Unit, Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
| | - G Starnini
- Belcolle Hospital, ASL Viterbo, Viterbo, Italy
| | | | | | - A R Ciccaglione
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - B Ensoli
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, V.le Regina Elena 299, 00161, Rome, Italy
| | - S Buttò
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, V.le Regina Elena 299, 00161, Rome, Italy
| |
Collapse
|
4
|
Salmona M, Lascoux-Combe C, Nere ML, Rubenstein E, Molina JM, Delaugerre C, Chaix ML. Transmission of S230R integrase drug resistance mutation affecting second-generation integrase inhibitors in a French primary HIV-1 infected man. J Antimicrob Chemother 2023:7153473. [PMID: 37147875 DOI: 10.1093/jac/dkad135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023] Open
Affiliation(s)
- Maud Salmona
- Virologie, Hôpital Saint-Louis, Assistance Publique Hôpitaux de Paris, Paris, France
- INSERM U976, Université Paris Cité, Hôpital Saint Louis, Paris 75010, France
| | - Caroline Lascoux-Combe
- Maladies Infectieuses, Hôpital Saint-Louis, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Marie Laure Nere
- Virologie, Hôpital Saint-Louis, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Emma Rubenstein
- Maladies Infectieuses, Hôpital Saint-Louis, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Jean Michel Molina
- Maladies Infectieuses, Hôpital Saint-Louis, Assistance Publique Hôpitaux de Paris, Paris, France
- INSERM U944, CNRS UMR 7212, Institut Universitaire d'Hématologie, Université Paris Cité, Hôpital Saint Louis, Paris 75010, France
| | - Constance Delaugerre
- Virologie, Hôpital Saint-Louis, Assistance Publique Hôpitaux de Paris, Paris, France
- INSERM U944, CNRS UMR 7212, Institut Universitaire d'Hématologie, Université Paris Cité, Hôpital Saint Louis, Paris 75010, France
| | - Marie Laure Chaix
- Virologie, Hôpital Saint-Louis, Assistance Publique Hôpitaux de Paris, Paris, France
- INSERM U944, CNRS UMR 7212, Institut Universitaire d'Hématologie, Université Paris Cité, Hôpital Saint Louis, Paris 75010, France
| |
Collapse
|
5
|
Fofana DB, Diarra H, Guindo I, Savadogo MK, d’Almeida M, Diallo FI, Baldé A, Soulié C, Kone A, Marcelin AG, Maiga AI, Lambert-Niclot S, Maiga M, McFall S, Hawkins CA, Murphy RL, Sylla M, Katlama C, Holl JL, Calvez V, Morand-Joubert L. Prevalence of HIV-1 Natural Polymorphisms and Integrase-Resistance-Associated Mutations in African Children. Viruses 2023; 15:v15020546. [PMID: 36851760 PMCID: PMC9964382 DOI: 10.3390/v15020546] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/05/2023] [Accepted: 02/12/2023] [Indexed: 02/18/2023] Open
Abstract
Integrase inhibitors (INIs) are a potent option for HIV treatment. Limited data exist on INI resistance in West Africa, particularly in children living with HIV/AIDS. We determined the prevalence of integrase gene polymorphisms and the frequency of naturally occurring amino acid (aa) substitutions at positions associated with INI resistance. Dried blood spot (DBS) samples were obtained from one hundred and seven (107) HIV-1-infected children aged less than 15 years old in two West African countries, Benin and Mali. All children were naïve to INI treatment, 56 were naïve to anti-retroviral therapy (ART), and 51 had received ART. Genetic sequencing of HIV integrase was successful in 75 samples. The aa changes at integrase positions associated with INI resistance were examined according to the Stanford HIV Genotypic Resistance database. The median ages were 2.6 and 10 years for ART-naïve and -treated children, respectively. The most common subtypes observed were CRF02_AG (74.7%) followed by CRF06_cpx (20%). No major INI-resistance mutations at positions 66, 92, 121, 143, 147, 148, 155, and 263 were detected. The most prevalent INI accessory resistance mutations were: L74I/M (14/75, 18.6%) followed by E157Q (8/75, 10.6%), G163E/N/T/Q (5/75, 6.6%), Q95A/H/P (2/75, 2.6%), and T97A (4/75, 5.3%). Other substitutions observed were M50I/L/P, H51E/P/S/Q, I72V, T112V, V201I, and T206S. Polymorphisms at positions which may influence the genetic barrier and/or drive the selection of specific INI-resistance pathways were detected. However, no transmitted drug resistance (TDR) to INI was detected among samples of INI-naïve patients. These findings support the use of this treatment class for children with HIV-1, particularly in West Africa.
Collapse
Affiliation(s)
- Djeneba B. Fofana
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-Hôpitaux de Paris (AP-HP), Saint-Antoine Hospital, F-75012 Paris, France
- Correspondence:
| | - Houdou Diarra
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | - Ibrahima Guindo
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | | | - Marceline d’Almeida
- Département Mère Enfant, Faculté Des Sciences De La Santé, Université Abomey-Calavi, CNHU—HKM, Cotonou 229, Benin
| | - Fatoumata I. Diallo
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | - Aliou Baldé
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
| | - Cathia Soulié
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-HÔpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, F-75013 Paris, France
| | - Amadou Kone
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-HÔpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, F-75013 Paris, France
| | - Almoustapha I. Maiga
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | - Sidonie Lambert-Niclot
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-Hôpitaux de Paris (AP-HP), Saint-Antoine Hospital, F-75012 Paris, France
| | - Mamoudou Maiga
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
- Institute for Global Health, Northwestern University, Chicago, IL 60208, USA
| | - Sally McFall
- Institute for Global Health, Northwestern University, Chicago, IL 60208, USA
| | - Claudia A. Hawkins
- Institute for Global Health, Northwestern University, Chicago, IL 60208, USA
| | - Robert L. Murphy
- Institute for Global Health, Northwestern University, Chicago, IL 60208, USA
| | - Mariam Sylla
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | - Christine Katlama
- Service des Maladies Infectieuses, Hôpital Pitié-Salpêtrière APHP, F-75013 Paris, France
| | - Jane L. Holl
- Biological Sciences Division, University of Chicago, Chicago, IL 60637, USA
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-HÔpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, F-75013 Paris, France
| | - Laurence Morand-Joubert
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-Hôpitaux de Paris (AP-HP), Saint-Antoine Hospital, F-75012 Paris, France
| |
Collapse
|
6
|
Ndashimye E, Reyes PS, Arts EJ. New antiretroviral inhibitors and HIV-1 drug resistance: more focus on 90% HIV-1 isolates? FEMS Microbiol Rev 2023; 47:fuac040. [PMID: 36130204 PMCID: PMC9841967 DOI: 10.1093/femsre/fuac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/13/2022] [Accepted: 09/18/2022] [Indexed: 01/21/2023] Open
Abstract
Combined HIV antiretroviral therapy (cART) has been effective except if drug resistance emerges. As cART has been rolled out in low-income countries, drug resistance has emerged at higher rates than observed in high income countries due to factors including initial use of these less tolerated cART regimens, intermittent disruptions in drug supply, and insufficient treatment monitoring. These socioeconomic factors impacting drug resistance are compounded by viral mechanistic differences by divergent HIV-1 non-B subtypes compared to HIV-1 subtype B that largely infects the high-income countries (just 10% of 37 million infected). This review compares the inhibition and resistance of diverse HIV-1 subtypes and strains to the various approved drugs as well as novel inhibitors in clinical trials. Initial sequence variations and differences in replicative fitness between HIV-1 subtypes pushes strains through different fitness landscapes to escape from drug selective pressure. The discussions here provide insight to patient care givers and policy makers on how best to use currently approved ART options and reduce the emergence of drug resistance in ∼33 million individuals infected with HIV-1 subtype A, C, D, G, and recombinants forms. Unfortunately, over 98% of the literature on cART resistance relates to HIV-1 subtype B.
Collapse
Affiliation(s)
- Emmanuel Ndashimye
- Department of Microbiology and Immunology, Western University Schulich School of Medicine & Dentistry, Western University, N6A 3K7, London, Ontario, Canada
- Joint Clinical Research Centre, -Center for AIDS Research Laboratories, 256, Kampala, Uganda
| | - Paul S Reyes
- Department of Microbiology and Immunology, Western University Schulich School of Medicine & Dentistry, Western University, N6A 3K7, London, Ontario, Canada
| | - Eric J Arts
- Department of Microbiology and Immunology, Western University Schulich School of Medicine & Dentistry, Western University, N6A 3K7, London, Ontario, Canada
| |
Collapse
|
7
|
Gil H, Delgado E, Benito S, Moreno-Lorenzo M, Thomson MM. Factors associated with HIV-1 resistance to integrase strand transfer inhibitors in Spain: Implications for dolutegravir-containing regimens. Front Microbiol 2022; 13:1051096. [PMID: 36578581 PMCID: PMC9792149 DOI: 10.3389/fmicb.2022.1051096] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/11/2022] [Indexed: 12/14/2022] Open
Abstract
Integrase strand transfer inhibitor (INSTI)-containing regimens in HIV-1-infected patients have experienced a global increase. Recently, WHO has emphasized the need to fast-track the transition to dolutegravir (DTG)-based antiretroviral (ARV) treatments. However, continued surveillance of INSTI resistance is recommended. In this study, clinical, epidemiological, and virological features associated with INSTI resistance diagnosed in Spain were analyzed. Samples collected between 2008 and 2021 from HIV-1-infected patients were analyzed in integrase, protease, and reverse transcriptase using Sanger population sequencing. ARV drug resistance was evaluated with the Stanford University HIVdb program. Among 2,696 patients, 174 (6.5%) had INSTI resistance, all of them to first-generation INSTIs, and 71 (2.6%) had also resistance to second-generation INSTIs. Of these, only 5 individuals were exposed to DTG as the only INSTI, in whom resistance development was associated with poor treatment adherence and/or resistance to other ARV classes. Of newly HIV-1-diagnosed individuals, 0.92% harbored INSTI-resistant viruses, with low prevalences maintained along time, and only one had low-level resistance to DTG. Persons who inject drugs, age over 39 years, resistance to other ARV classes, and longer time from diagnosis were associated with INSTI resistance (p < 0.001). Non-subtype B INSTI-resistant viruses lacked the Q148H + G140S resistance pathway and showed lower INSTI resistance levels than subtype B viruses. In conclusion, INSTI resistance is uncommon and associated with long-term infections, older age and additional resistance to other ARV drug classes, and is rare in newly diagnosed HIV-1 infections. Our results also support the preferential use of DTG-containing regimens in first-line treatments, although surveillance of INSTI resistance is encouraged.
Collapse
|
8
|
Aulicino PC, Momin Z, Rozenszajn M, Monzon A, Arazi-Caillaud S, Bologna R, Mangano A, Kimata JT. HIV-1 subtype F integrase polymorphisms external to the catalytic core domain contribute to severe loss of replication capacity in context of the integrase inhibitor resistance mutation Q148H. J Antimicrob Chemother 2022; 77:2793-2802. [PMID: 35897124 PMCID: PMC9989736 DOI: 10.1093/jac/dkac238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/20/2022] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND In prior studies, HIV-1 BF recombinants with subtype F integrases failed to develop resistance to raltegravir through the Q148H mutational pathway. We aimed to determine the role of subtype-specific polymorphisms in integrase on drug susceptibility, viral replication and integration. METHODS Integrase sequences were retrieved from the Los Alamos Database or obtained from the Garrahan HIV cohort. HIV-1 infectious molecular clones with or without Q148H (+ G140S) resistance mutations were constructed using integrases of subtype B (NL4-3) or F1(BF) ARMA159 and URTR23. Integrase chimeras were generated by reciprocal exchanges of a 200 bp fragment spanning amino acids 85-150 of the catalytic core domain (CCD) of NL4-3-Q148H and either ARMA159-Q148H or URTR23-Q148H. Viral infections were quantified by p24 ELISA and Alu-gag integration PCR assay. RESULTS At least 18 different polymorphisms distinguish subtype B from F1(BF) recombinant integrases. In phenotypic experiments, p24 at Day 15 post-infection was high (105-106 pg/mL) for WT and NL4-3-Q148H; by contrast, it was low (102-104 pg/mL) for both F1(BF)-Q148H + G140S viruses, and undetectable for the Q148H mutants. Compared with WT viruses, integrated DNA was reduced by 5-fold for NL4-3-Q148H (P = 0.05), 9-fold for URTR23-Q148H (P = 0.01) and 16000-fold for ARMA159-Q148H (P = 0.01). Reciprocal exchange between B and F1(BF) of an integrase CCD region failed to rescue the replicative defect of F1(BF) integrase mutants. CONCLUSIONS The functional impairment of Q148H in the context of subtype F integrases from BF recombinants explains the lack of selection of this pathway in vivo. Non-B polymorphisms external to the integrase CCD may influence the pathway to integrase strand transfer inhibitor resistance.
Collapse
Affiliation(s)
- Paula C Aulicino
- Laboratory of Cellular Biology and Retroviruses, Unit of Virology and Molecular Epidemiology, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Zoha Momin
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Mijael Rozenszajn
- Laboratory of Cellular Biology and Retroviruses, Unit of Virology and Molecular Epidemiology, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Arturo Monzon
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Solange Arazi-Caillaud
- Unit of Epidemiology and Infectology, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Buenos Aires, Argentina
| | - Rosa Bologna
- Unit of Epidemiology and Infectology, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Buenos Aires, Argentina
| | - Andrea Mangano
- Laboratory of Cellular Biology and Retroviruses, Unit of Virology and Molecular Epidemiology, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Jason T Kimata
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|
9
|
Pre-Treatment Integrase Inhibitor Resistance and Natural Polymorphisms among HIV-1 Subtype C Infected Patients in Ethiopia. Viruses 2022; 14:v14040729. [PMID: 35458459 PMCID: PMC9029575 DOI: 10.3390/v14040729] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/18/2022] [Accepted: 03/28/2022] [Indexed: 02/01/2023] Open
Abstract
Dolutegravir-based antiretroviral therapy (ART) has been scaled up in many developing countries, including Ethiopia. However, subtype-dependent polymorphic differences might influence the occurrence of HIV-drug-resistance mutations (HIVDRMs). We analyzed the prevalence of pre-treatment integrase strand transfer inhibitor (INSTI) HIVDRMs and naturally occurring polymorphisms (NOPs) of the integrase gene, using plasma samples collected as part of the national HIVDR survey in Ethiopia in 2017. We included a total of 460 HIV-1 integrase gene sequences from INSTI-naïve (n = 373 ART-naïve and n = 87 ART-experienced) patients. No dolutegravir-associated HIVDRMs were detected, regardless of previous exposure to ART. However, we found E92G in one ART-naïve patient specimen and accessory mutations in 20/460 (4.3%) of the specimens. Moreover, among the 288 integrase amino acid positions of the subtype C, 187/288 (64.9%) were conserved (<1.0% variability). Analysis of the genetic barrier showed that the Q148H/K/R dolutegravir resistance pathway was less selected in subtype C. Docking analysis of the dolutegravir showed that protease- and reverse-transcriptase-associated HIVDRMs did not affect the native structure of the HIV-1 integrase. Our results support the implementation of a wide scale-up of dolutegravir-based regimes. However, the detection of polymorphisms contributing to INSTI warrants the continuous surveillance of INSTI resistance.
Collapse
|
10
|
Sayan M, Yildirim FS, Akhan S, Karaoglan I, Akalin H. Integrase Strand Transfer Inhibitor (INSTI) Genotypic Resistance Analysis in Treatment-nNaive, INSTI Free Antiretroviral-Experienced and INSTI-Experienced Turkish Patients Infected with HIV-1. Curr HIV Res 2022; 20:184-192. [PMID: 35240975 DOI: 10.2174/1570162x20666220303104509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 01/10/2022] [Accepted: 01/28/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND AND OBJECTIVE Integrase strand transfer inhibitors (INSTIs) are currently the standard of practice for first-line HIV therapy for most patients. We evaluated the mutations associated with INSTI resistance in naive HIV-1 infected patients and treated them with antiretrovirals (ART). METHODS The study, conducted in the 2018 - 2020 period, included 50 ART-naïve patients, 69 INSTI free ART-experienced patients, and 82 INSTI-experienced patients. INSTI resistance mutations were interpreted using the Stanford University HIVdb Program algorithm. RESULTS INSTI resistance was not detected in ART naïve patients. At least one INSTI resistance mutation was detected in 10% of the INSTI-free patients and 29% of the INSTI-treated patients. Major INSTI-mutations E138K, Y143R, S147G, Q148R, N155H, and E157Q were found in raltegravir. Additional mutations, E92Q, E138K, G140A, S147G, and Q148R were found in elvitegravir; E192Q, E138K/T, G140A/S, S147G, Q148H/R, N155H, E157Q were found in dolutegravir (DTG) experienced patients. According to all drug classes, drug resistance mutation prevalences were determined at the rate of 60%, 46%, and 46% in the RAL, EVG, and DTG groups, respectively. CONCLUSION Our findings provide data for treatment and resistance management of INSTIs and may provide feedback for INSTIs resistance surveillance consensus-building efforts. In viral rebound under INSTI treatment, INSTI-resistant mutations follow typical INSTI resistance pathways and high resistance rates. INSTI resistance genotypic analysis should be considered before any DTG-based regimes can be initiated in the future, and reduced DTG susceptibility should be carefully monitored and investigated.
Collapse
Affiliation(s)
- Murat Sayan
- Kocaeli University, Research and Education Hospital, PCR Laboratory, Kocaeli, Turkey
- Near East University, DESAM Research Institute, Nicosia, Northern Cyprus
| | - Figen Sarigul Yildirim
- Health Sciences University, Antalya Research and Education Hospital, Department of Infectious Diseases, Antalya, Turkey
| | - Sila Akhan
- Kocaeli University, Medical Faculty, Department of Infectious Diseases and Clinical Microbiology, Kocaeli, Turkey
| | - Ilkay Karaoglan
- Gaziantep University, Medical Faculty, Department of Infectious Diseases and Clinical Microbiology, Gaziantep, Turkey
| | - Halis Akalin
- Uludağ University, Medical Faculty, Department of Infectious Diseases and Clinical Microbiology, Bursa, Turkey
| |
Collapse
|
11
|
Rhee SY, Kassaye SG, Jordan MR, Kouamou V, Katzenstein D, Shafer RW. Public availability of HIV-1 drug resistance sequence and treatment data: a systematic review. THE LANCET MICROBE 2022; 3:e392-e398. [PMID: 35544100 PMCID: PMC9095989 DOI: 10.1016/s2666-5247(21)00250-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 08/12/2021] [Accepted: 09/06/2021] [Indexed: 11/28/2022] Open
Abstract
HIV-1 pol sequences from antiretroviral therapy (ART)-naive and ART-experienced people living with HIV-1 are fundamental to understanding the genetic correlates and epidemiology of HIV-1 drug resistance (HIVDR). To assess the public availability of HIV-1 pol sequences and ART histories of the individuals from whom sequenced viruses were obtained, we performed a systematic review of PubMed and GenBank for HIVDR studies published between 2010 and 2019 that reported HIV-1 pol sequences. 934 studies met inclusion criteria, including 461 studies of ART-naive adults, 407 of ART-experienced adults, and 66 of ART-naive and ART-experienced children. Sequences were available for 317 (68·8%) studies of ART-naive individuals, 190 (46·7%) of ART-experienced individuals, and 45 (68·2%) of children. Among ART-experienced individuals, sequences plus linked ART histories were available for 82 (20·1%) studies. Sequences were available for 21 (29·2%) of 72 clinical trials. Among journals publishing more than ten studies, the proportion with available sequences ranged from 8·3% to 86·9%. Strengthened implementation of data sharing policies is required to increase the number of studies with available HIVDR data to support the enterprise of global ART in the face of emerging HIVDR. the Lancet Group takes a neutral position with respect to territorial claims in published maps and institutional affiliations.
Collapse
Affiliation(s)
- Soo-Yon Rhee
- Department of Medicine, Stanford University, Stanford, CA, USA.
| | - Seble G Kassaye
- Department of Medicine, Georgetown University, Washington, DC, USA
| | - Michael R Jordan
- Levy Center for Integrated Management of Antimicrobial Resistance, Tufts University, Boston, MA, USA; Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA, USA
| | - Vinie Kouamou
- Unit of Medicine, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - David Katzenstein
- Department of Molecular Biology, Biomedical Research and Training Institute, Harare, Zimbabwe
| | - Robert W Shafer
- Department of Medicine, Stanford University, Stanford, CA, USA
| |
Collapse
|
12
|
Semengue ENJ, Armenia D, Inzaule S, Santoro MM, Dambaya B, Takou D, Teto G, Nka AD, Yagai B, Fabeni L, Chenwi C, Angong Beloumou G, Djupsa Ndjeyep SC, Colizzi V, Perno CF, Ceccherini-Silberstein F, Fokam J. Baseline integrase drug resistance mutations and conserved regions across HIV-1 clades in Cameroon: implications for transition to dolutegravir in resource-limited settings. J Antimicrob Chemother 2021; 76:1277-1285. [PMID: 33501504 DOI: 10.1093/jac/dkab004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/28/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Transition to dolutegravir-based regimens in resource-limited settings (RLS) requires prior understanding of HIV-1 integrase variants and conserved regions. Therefore, we evaluated integrase drug resistance mutations (DRMs) and conserved regions amongst integrase strand transfer inhibitor (INSTI)-naive patients harbouring diverse HIV-1 clades in Cameroon. METHODS A cross-sectional study was conducted amongst 918 INSTI-naive patients from Cameroon (89 ART-naive and 829 ART-experienced patients). HIV-1 sequences were interpreted regarding INSTI-DRMs using the Stanford HIVdb v8.9-1 and the 2019 IAS-USA list. Amino acid positions with <1% variability were considered as highly conserved. Subtyping was performed by phylogeny. RESULTS Overall prevalence (95% CI) of INSTI-DRMs was 0.8% (0.4-1.7), with 0.0% (0.0-4.0) amongst ART-naive versus 0.9% (0.5-1.9) amongst ART-experienced patients; P = 0.44. Accessory mutations (95% CI) were found in 33.8% (30.9-37.0), with 38.2% (28.1-49.1) amongst ART-naive versus 33.4% (30.4-36.7) amongst ART-experienced patients; P = 0.21. Of 288 HIV-1 integrase amino acid positions, 58.3% were highly conserved across subtypes in the following major regions: V75-G82, E85-P90, H114-G118, K127-W132, E138-G149, Q168-L172, T174-V180, W235-A239 and L241-D253. Wide genetic diversity was found (37 clades), including groups M (92.3%), N (1.4%), O (6.2%) and P (0.1%). Amongst group M, CRF02_AG was predominant (47.4%), with a significantly higher frequency (95% CI) of accessory mutations compared with non-AG [41.4% (36.8-46.0) versus 27.1% (23.3-31.2) respectively; P < 0.001]. CONCLUSIONS The low baseline of INSTI-DRMs (<1%) in Cameroon suggests effectiveness of dolutegravir-based regimens. In spite of high conservation across clades, the variability of accessory mutations between major circulating strains underscores the need for monitoring the selection of INSTI-DRMs while scaling up dolutegravir-based regimens in RLS.
Collapse
Affiliation(s)
- Ezechiel Ngoufack Jagni Semengue
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.,Evangelical University of Cameroon, Bandjoun, Cameroon
| | - Daniele Armenia
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.,Saint Camillus International University of Health and Medical Sciences, Rome, Italy
| | - Seth Inzaule
- Department of Global Health, Academic Medical Center of the University of Amsterdam and Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
| | | | - Béatrice Dambaya
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Faculty of Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Désiré Takou
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Georges Teto
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Alex Durand Nka
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.,Evangelical University of Cameroon, Bandjoun, Cameroon
| | - Bouba Yagai
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Lavinia Fabeni
- Laboratory of Virology, National Institute for Infectious Diseases "Lazzaro Spallanzani" - IRCCS, Rome, Italy
| | - Collins Chenwi
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Grâce Angong Beloumou
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Sandrine Claire Djupsa Ndjeyep
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Vittorio Colizzi
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.,Evangelical University of Cameroon, Bandjoun, Cameroon
| | - Carlo-Federico Perno
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Bambino Gesu Children's Hospital, IRCCS, Rome, Italy
| | | | - Joseph Fokam
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon.,National HIV Drug Resistance Working Group, Ministry of Public Health, Cameroon.,Faculty of Health Sciences, University of Buea, Buea, Cameroon
| |
Collapse
|
13
|
Mbisa JL, Ledesma J, Kirwan P, Bibby DF, Manso C, Skingsley A, Murphy G, Brown A, Dunn DT, Delpech V, Geretti AM. Surveillance of HIV-1 transmitted integrase strand transfer inhibitor resistance in the UK. J Antimicrob Chemother 2021; 75:3311-3318. [PMID: 32728703 PMCID: PMC7566560 DOI: 10.1093/jac/dkaa309] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/15/2020] [Indexed: 12/16/2022] Open
Abstract
Background HIV treatment guidelines have traditionally recommended that all HIV-positive individuals are tested for evidence of drug resistance prior to starting ART. Testing for resistance to reverse transcriptase inhibitors and PIs is well established in routine care. However, testing for integrase strand transfer inhibitor (InSTI) resistance is less consistent. Objectives To inform treatment guidelines by determining the prevalence of InSTI resistance in a national cohort of recently infected individuals. Patients and methods Recent (within 4 months) HIV-1 infections were identified using a Recent Infection Testing Algorithm of new HIV-1 diagnoses in the UK. Resistance-associated mutations (RAMs) in integrase, protease and reverse transcriptase were detected by ultradeep sequencing, which allows for the sensitive estimation of the frequency of each resistant variant in a sample. Results The analysis included 655 randomly selected individuals (median age = 33 years, 95% male, 83% MSM, 78% white) sampled in the period 2014 to 2016 and determined to have a recent infection. These comprised 320, 138 and 197 samples from 2014, 2015 and 2016, respectively. None of the samples had major InSTI RAMs occurring at high variant frequency (≥20%). A subset (25/640, 3.9%) had major InSTI RAMs occurring only as low-frequency variants (2%–20%). In contrast, 47/588 (8.0%) had major reverse transcriptase inhibitor and PI RAMs at high frequency. Conclusions Between 2014 and 2016, major InSTI RAMs were uncommon in adults with recent HIV-1 infection, only occurring as low-frequency variants of doubtful clinical significance. Continued surveillance of newly diagnosed patients for evidence of transmitted InSTI resistance is recommended to inform clinical practice.
Collapse
Affiliation(s)
- Jean L Mbisa
- National Infection Service, Public Health England, London, UK.,National Institute for Health Research (NIHR) Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, UK
| | - Juan Ledesma
- National Infection Service, Public Health England, London, UK.,National Institute for Health Research (NIHR) Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, UK
| | - Peter Kirwan
- National Infection Service, Public Health England, London, UK
| | - David F Bibby
- National Infection Service, Public Health England, London, UK
| | - Carmen Manso
- National Infection Service, Public Health England, London, UK
| | | | - Gary Murphy
- National Infection Service, Public Health England, London, UK
| | - Alison Brown
- National Infection Service, Public Health England, London, UK
| | - David T Dunn
- Institute for Global Health, University College London, London, UK
| | - Valerie Delpech
- National Infection Service, Public Health England, London, UK.,National Institute for Health Research (NIHR) Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, UK
| | - Anna Maria Geretti
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| |
Collapse
|
14
|
Ndashimye E, Avino M, Olabode AS, Poon AFY, Gibson RM, Li Y, Meadows A, Tan C, Reyes PS, Kityo CM, Kyeyune F, Nankya I, Quiñones-Mateu ME, Arts EJ. Accumulation of integrase strand transfer inhibitor resistance mutations confers high-level resistance to dolutegravir in non-B subtype HIV-1 strains from patients failing raltegravir in Uganda. J Antimicrob Chemother 2021; 75:3525-3533. [PMID: 32853364 DOI: 10.1093/jac/dkaa355] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/03/2020] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Increasing first-line treatment failures in low- and middle-income countries (LMICs) have led to increased use of integrase strand transfer inhibitors (INSTIs) such as dolutegravir. However, HIV-1 susceptibility to INSTIs in LMICs, especially with previous raltegravir exposure, is poorly understood due to infrequent reporting of INSTI failures and testing for INSTI drug resistance mutations (DRMs). METHODS A total of 51 non-subtype B HIV-1 infected patients failing third-line (raltegravir-based) therapy in Uganda were initially selected for the study. DRMs were detected using Sanger and deep sequencing. HIV integrase genes of 13 patients were cloned and replication capacities (RCs) and phenotypic susceptibilities to dolutegravir, raltegravir and elvitegravir were determined with TZM-bl cells. Spearman's correlation coefficient was used to determine cross-resistance between INSTIs. RESULTS INSTI DRMs were detected in 47% of patients. HIV integrase-recombinant virus carrying one primary INSTI DRM (N155H or Y143R/S) was susceptible to dolutegravir but highly resistant to raltegravir and elvitegravir (>50-fold change). Two patients, one with E138A/G140A/Q148R/G163R and one with E138K/G140A/S147G/Q148K, displayed the highest reported resistance to raltegravir, elvitegravir and even dolutegravir. The former multi-DRM virus had WT RC whereas the latter had lower RCs than WT. CONCLUSIONS In HIV-1 subtype A- and D-infected patients failing raltegravir and harbouring INSTI DRMs, there is high-level resistance to elvitegravir and raltegravir. More routine monitoring of INSTI treatment may be advised in LMICs, considering that multiple INSTI DRMs may have accumulated during prolonged exposure to raltegravir during virological failure, leading to high-level INSTI resistance, including dolutegravir resistance.
Collapse
Affiliation(s)
- Emmanuel Ndashimye
- Department of Microbiology and Immunology, Western University, London, Canada.,Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Mariano Avino
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - Abayomi S Olabode
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - Art F Y Poon
- Department of Microbiology and Immunology, Western University, London, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, Canada.,Department of Applied Mathematics, Western University, London, Canada
| | - Richard M Gibson
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Yue Li
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Adam Meadows
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Christine Tan
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Paul S Reyes
- Department of Microbiology and Immunology, Western University, London, Canada
| | | | - Fred Kyeyune
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Immaculate Nankya
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | | | - Eric J Arts
- Department of Microbiology and Immunology, Western University, London, Canada
| |
Collapse
|
15
|
Sánchez D, Arazi Caillaud S, Zapiola I, Fernandez Giuliano S, Bologna R, Mangano A, Aulicino PC. Impact of genotypic diversity on selection of subtype-specific drug resistance profiles during raltegravir-based therapy in individuals infected with B and BF recombinant HIV-1 strains. J Antimicrob Chemother 2021; 75:1567-1574. [PMID: 32125378 DOI: 10.1093/jac/dkaa042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/08/2020] [Accepted: 01/20/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Current knowledge on HIV-1 resistance to integrase inhibitors (INIs) is based mostly on subtype B strains. This contrasts with the increasing use of INIs in low- and middle-income countries, where non-B subtypes predominate. MATERIALS AND METHODS HIV-1 drug resistance genotyping was performed in 30 HIV-1-infected individuals undergoing virological failure to raltegravir. Drug resistance mutations (DRMs) and HIV-1 subtype were characterized using Stanford HIVdb and phylogenetic analyses. RESULTS Of the 30 integrase (IN) sequences, 14 were characterized as subtype F (47%), 8 as subtype B (27%), 7 as BF recombinants (23%) and 1 as a putative CRF05_DF (3%). In 25 cases (83%), protease and reverse transcriptase (PR-RT) sequences from the same individuals confirmed the presence of different BF recombinants. Stanford HIVdb genotyping was concordant with phylogenetic inference in 70% of IN and 60% of PR-RT sequences. INI DRMs differed between B and F IN subtypes, with Q148K/R/H, G140S and E138K/A being more prevalent in subtype B (63% versus 0%, P = 0.0021; 50% versus 0%, P = 0.0096; and 50% versus 0%, P = 0.0096, respectively). These differences were independent of the time on raltegravir therapy or viral load at the time of genotyping. INI DRMs in subtype F IN genomes predicted a lower level of resistance to raltegravir and no cross-resistance to second-generation INIs. CONCLUSIONS Alternative resistance pathways to raltegravir develop in subtypes B and F IN genomes, with implications for clinical practice. Evaluating the role of HIV-1 subtype in development and persistence of mutations that confer resistance to INIs will be important to improve algorithms for resistance testing and optimize the use of INIs.
Collapse
Affiliation(s)
- Daniela Sánchez
- Laboratorio de Biología Celular y Retrovirus-CONICET, Unidad de Virología y Epidemiología Molecular, Hospital de Pediatría "Juan P. Garrahan", Buenos Aires, Argentina.,Centro Provincial VIH/SIDA y Hepatitis Virales de la Provincia de Buenos Aires, Instituto Biológico Dr Tomás Perón, La Plata, Argentina
| | - Solange Arazi Caillaud
- Servicio de Epidemiología e Infectología, Hospital de Pediatría "Juan P. Garrahan", Buenos Aires, Argentina
| | - Ines Zapiola
- Unidad de Virología, Hospital de Infecciosas "Francisco J. Muñiz", Buenos Aires, Argentina
| | | | - Rosa Bologna
- Servicio de Epidemiología e Infectología, Hospital de Pediatría "Juan P. Garrahan", Buenos Aires, Argentina
| | - Andrea Mangano
- Laboratorio de Biología Celular y Retrovirus-CONICET, Unidad de Virología y Epidemiología Molecular, Hospital de Pediatría "Juan P. Garrahan", Buenos Aires, Argentina
| | - Paula C Aulicino
- Laboratorio de Biología Celular y Retrovirus-CONICET, Unidad de Virología y Epidemiología Molecular, Hospital de Pediatría "Juan P. Garrahan", Buenos Aires, Argentina
| |
Collapse
|
16
|
Marcelin AG, Charpentier C, Bellecave P, Abdi B, Chaix ML, Ferre V, Raymond S, Fofana D, Bocket L, Mirand A, Le Guillou-Guillemette H, Montes B, Amiel C, Pallier C, Fafi-Kremer S, De Monte A, Alessandri-Gradt E, Scholtes C, Maillard A, Jeulin H, Bouvier-Alias M, Roussel C, Dos Santos G, Signori-Schmuck A, Dina J, Vallet S, Stefic K, Soulié C, Calvez V, Descamps D, Flandre P. Factors associated with the emergence of integrase resistance mutations in patients failing dual or triple integrase inhibitor-based regimens in a French national survey. J Antimicrob Chemother 2021; 76:2400-2406. [PMID: 34100068 DOI: 10.1093/jac/dkab193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/11/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Successful 2-drug regimens (2DRs) for HIV were made possible by the availability of drugs combining potency and tolerability with a high genetic barrier to resistance. How these deal with resistance development/re-emergence, compared with 3DRs, is thus of paramount importance. MATERIALS AND METHODS A national survey including patients who were either naive or experienced with any 2DR or 3DR but failing integrase strand transfer inhibitor (INSTI)-containing regimens [two consecutive plasma viral load (VL) values >50 copies/mL] was conducted between 2014 and 2019. Genotypic resistance tests were interpreted with the v28 ANRS algorithm. RESULTS Overall, 1104 patients failing any INSTI-containing regimen (2DRs, n = 207; 3DRs, n = 897) were analysed. Five hundred and seventy-seven (52.3%) patients were infected with a B subtype and 527 (47.3%) with non-B subtypes. Overall, 644 (58%) patients showed no known integrase resistance mutations at failure. In multivariate analysis, factors associated with the emergence of at least one integrase mutation were: high VL at failure (OR = 1.24 per 1 log10 copies/mL increase); non-B versus B subtype (OR = 1.75); low genotypic sensitivity score (GSS) (OR = 0.10 for GSS = 2 versus GSS = 0-0.5); and dolutegravir versus raltegravir (OR = 0.46). Although 3DRs versus 2DRs reached statistical significance in univariate analysis (OR = 0.59, P = 0.007), the variable is not retained in the final model. CONCLUSIONS This study is one of the largest studies characterizing integrase resistance in patients failing any INSTI-containing 2DR or 3DR in routine clinical care and reveals factors associated with emergence of integrase resistance that should be taken into consideration in clinical management. No difference was evidenced between patients receiving a 2DR or a 3DR.
Collapse
Affiliation(s)
- Anne-Genevieve Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière-Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Charlotte Charpentier
- Service de Virologie, Université de Paris INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude-Bernard, F-75018 Paris, France
| | - Pantxika Bellecave
- CHU de Bordeaux, Laboratoire de Virologie, Univ. Bordeaux, CNRS UMR 5234, F-33076 Bordeaux, France
| | - Basma Abdi
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière-Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Marie-Laure Chaix
- INSERM U941, Université de Paris, Laboratoire de Virologie, AP-HP, Hôpital Saint-Louis, Paris, France
| | - Virginie Ferre
- CHU Nantes, Laboratoire de Virologie, CIC INSERM 143, F-44093 Nantes, France
| | - Stephanie Raymond
- INSERM UMR 1291 Toulouse, F-31300 France and Laboratoire de Virologie, CHU Toulouse Purpan, F-31300 Toulouse, France
| | - Djeneba Fofana
- AP-HP, CHU Saint Antoine, INSERM-Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1136, F-75012 Paris, France
| | - Laurence Bocket
- Univ. Lille, CHU Lille, Laboratoire de Virologie, Lille, France
| | | | | | - Brigitte Montes
- Laboratoire de Virologie, CHU Montpellier, Univ Montpellier, France
| | | | | | | | | | | | - Caroline Scholtes
- INSERM U1052, CRCL, Université de Lyon, Laboratoire de Virologie, Lyon, France
| | - Anne Maillard
- Laboratoire de Virologie, CHU de Rennes, Rennes, France
| | - Helene Jeulin
- Laboratoire de Virologie, CHRU de Nancy Brabois, Vandoeuvre-lès-Nancy, France
| | | | | | | | | | - Julia Dina
- Normandie Univ, UNICAEN, UNIROUEN, GRAM 2.0, Caen University Hospital Department of Virology, F-14000, Caen, France
| | - Sophie Vallet
- Laboratoire de Virologie, CHRU de Brest, Brest, France
| | - Karl Stefic
- INSERM U1259, Université de Tours et Laboratoire de Virologie, CHRU de Tours, Tours, France
| | - Cathia Soulié
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière-Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière-Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Diane Descamps
- CHU de Bordeaux, Laboratoire de Virologie, Univ. Bordeaux, CNRS UMR 5234, F-33076 Bordeaux, France
| | - Philippe Flandre
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | | |
Collapse
|
17
|
Young N, Hobbs M, Rahnama F, Shi J, Briggs S. An observational study of high- and low-abundance anti-retroviral resistance mutations among treatment-naïve people living with HIV in New Zealand between 2012 and 2017. Intern Med J 2021; 50:872-876. [PMID: 32656973 DOI: 10.1111/imj.14899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/20/2019] [Accepted: 12/21/2019] [Indexed: 11/29/2022]
Abstract
HIV resistance genotyping detects drug resistance mutations (DRMs) in ≥20% of circulating virus within an infected individual (high-abundance DRMs). Deep sequencing also detects DRMs in smaller viral subpopulations (low-abundance DRMs), although these are of uncertain importance. In this retrospective analysis of 292 treatment-naïve patients, high-abundance DRMs were present in 30/292 (10%) patients, but only one (0.3%) had resistance to first-line anti-retrovirals. Low-abundance DRMs were present in 36/247 (15%) patients, but none who received anti-retrovirals for which these were present had virologic failure. These findings demonstrate that starting first-line therapy in treatment-naïve patients need not be delayed while awaiting resistance testing.
Collapse
Affiliation(s)
- Nicholas Young
- Infectious Diseases Service, Auckland City Hospital, Auckland, New Zealand
| | - Mark Hobbs
- Infectious Diseases Service, Auckland City Hospital, Auckland, New Zealand
| | - Fahimeh Rahnama
- Virology Laboratory, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Jinyang Shi
- Virology Laboratory, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Simon Briggs
- Infectious Diseases Service, Auckland City Hospital, Auckland, New Zealand
| |
Collapse
|
18
|
Modica S, Redi D, Gagliardini R, Giombini E, Bezenchek A, Di Carlo D, Maggiolo F, Lombardi F, Borghetti A, Farinacci D, Callegaro A, Gismondo MR, Colafigli M, Sterrantino G, Costantini A, Ferrara SM, Rusconi S, Zazzi M, Rossetti B, De Luca A, Gianotti N. Impact of NRTI resistance mutations on virological effectiveness of antiretroviral regimens containing elvitegravir: a multi-cohort study. J Antimicrob Chemother 2021; 75:194-199. [PMID: 31605107 DOI: 10.1093/jac/dkz424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 09/04/2019] [Accepted: 09/10/2019] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Antiretroviral drug resistance mutations remain a major cause of treatment failure. OBJECTIVES To evaluate the impact of NRTI resistance mutations on virological effectiveness of elvitegravir-containing regimens. MATERIALS AND METHODS We selected treatment-experienced HIV-1-infected patients starting elvitegravir/cobicistat/emtricitabine/tenofovir alafenamide (E/C/F/TAF) or elvitegravir/cobicistat/emtricitabine/tenofovir disoproxil fumarate (E/C/F/TDF), with at least one protease/reverse transcriptase genotype available before switching and at least one HIV-1 RNA viral load (VL) measurement during follow-up. The primary endpoint was virological failure (VF), defined as one VL value of ≥1000 copies/mL or two consecutive VL values of >50 copies/mL. RESULTS We included 264 ART regimens: 75.6% male, median (IQR) age 47 years (39-53), 7 years (3-16) of HIV infection, nadir CD4+ 247 cells/mm3 (105-361), 81.5% with VL ≤50 copies/mL and 11.7% with at least one NRTI mutation at baseline. Eleven (5.2%) VFs occurred in virologically suppressed patients versus eight (15.1%) in viraemic patients. The estimated probability of VF at 48 weeks with versus without any NRTI mutation was 7.4% (95% CI 2.3-12.5) versus 3.8% (2.1-5.5) in virologically suppressed patients and 66.7% (39.5-93.9) versus 11.2% (6.5-15.9) (P<0.001) in viraemic patients. The only predictor of VF was time on therapy (per 1 year more, adjusted HR 1.14, 95% CI 1.02-1.27, P=0.024) in viraemic patients. CONCLUSIONS A switch to E/C/F/TDF or E/C/F/TAF is safe for virologically suppressed patients without documented NRTI resistance, but not recommended in viraemic patients with a history of NRTI resistance. Although we did not detect a detrimental effect of past NRTI resistance in virologically suppressed patients, a fully active regimen remains preferred in this setting due to possible rebound of drug-resistant virus in the long term.
Collapse
Affiliation(s)
- Sara Modica
- Department of Medical Biotechnologies, University of Siena, Viale Bracci, 16, 53100, Siena, Italy
| | - David Redi
- Department of Medical Biotechnologies, University of Siena, Viale Bracci, 16, 53100, Siena, Italy.,Infectious Diseases Unit, AOU Senese, Viale Bracci, 16, 53100, Siena, Italy
| | - Roberta Gagliardini
- National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Via Portuense, 292, 00161, Rome, Italy
| | - Emanuela Giombini
- National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Via Portuense, 292, 00161, Rome, Italy
| | | | - Domenico Di Carlo
- University of Milan, Pediatric Clinical Research Center 'Romeo and Enrica Invernizzi', Via Giovanni Battista Grassi, 74, 20157, Milan, Italy
| | - Franco Maggiolo
- Infectious Diseases Unit, Ospedali Riuniti, Largo Barozzi, 1, 24128, Bergamo, Italy
| | - Francesca Lombardi
- UOC Malattie Infettive, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli 8, 00168, Roma, Italia
| | - Alberto Borghetti
- UOC Malattie Infettive, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli 8, 00168, Roma, Italia
| | - Damiano Farinacci
- UOC Malattie Infettive, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli 8, 00168, Roma, Italia
| | - Annapaola Callegaro
- Microbiology and Virology Unit, Bergamo Hospital, Piazza OMS, 1, 24127, Bergamo, Italy
| | - Maria R Gismondo
- Microbiology Unit, Ospedale L. Sacco, Via G.B Grassi, 74, 20157, Milan, Italy
| | - Manuela Colafigli
- San Gallicano Dermatologic Institute, STI/HIV Unit, IRCCS, via Elio Chianesi, 53, 00144, Rome, Italy
| | - Gaetana Sterrantino
- Department di Clinical and Experimental Medicine, Clinic of Tropical and Infectious Diseases, University of Florence, Largo Brambilla, 3, 50134, Florence, Italy
| | - Andrea Costantini
- Clinical Immunology Unit, Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Via Tronto, 10, 60121, Ancona, Italy
| | - Sergio M Ferrara
- Clinic of Infectious Diseases, Azienda ospedaliera-Universitaria Ospedali Riuniti, Viale Luigi Pinto, 1, 71122, Foggia, Italy
| | - Stefano Rusconi
- Infectious and Tropical Diseases Unit, DIBIC L. Sacco Hospital, University of Milano, Via G.B Grassi, 74, 20157, Milan, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Viale Bracci, 16, 53100, Siena, Italy
| | - Barbara Rossetti
- Infectious Diseases Unit, AOU Senese, Viale Bracci, 16, 53100, Siena, Italy
| | - Andrea De Luca
- Department of Medical Biotechnologies, University of Siena, Viale Bracci, 16, 53100, Siena, Italy.,Infectious Diseases Unit, AOU Senese, Viale Bracci, 16, 53100, Siena, Italy
| | - Nicola Gianotti
- Infectious Diseases, IRCCS San Raffaele, Via Olgettina 60, 20132, Milan, Italy
| |
Collapse
|
19
|
Lai A, Franzetti M, Bergna A, Saladini F, Bruzzone B, Di Giambenedetto S, Di Biagio A, Lo Caputo S, Santoro MM, Maggiolo F, Parisi SG, Rusconi S, Gianotti N, Balotta C. Marked decrease in acquired resistance to antiretrovirals in latest years in Italy. Clin Microbiol Infect 2020; 27:1038.e1-1038.e6. [PMID: 32979570 DOI: 10.1016/j.cmi.2020.09.028] [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: 01/24/2020] [Revised: 08/25/2020] [Accepted: 09/15/2020] [Indexed: 11/25/2022]
Abstract
OBJECTIVES The aim of this study was to evaluate acquired drug resistance in Italy in the 2009-2018 period. METHODS We analysed 3094 patients from the Italian ARCA database who had failed antiretroviral treatment and who had received a genotypic test after 6 months of treatment. Drug resistance mutations were identified using International AIDS Society (IAS)-USA tables and the Stanford HIVdb algorithm. The global burden of acquired resistance was calculated among all subjects with antiretroviral failure. Time trends and correlates of resistance were analysed using standard statistical tests. RESULTS Patients of non-European origin and non-B subtypes increased significantly from 11.5% (103/896) to 19.2% (33/172) and from 13.1% (141/1079) to 23.8% (53/223), respectively, over time. Overall, 14.5% (448/3094), 12.1% (374/3094) and 37.8% (1169/3094) of patients failed first, second and later lines, respectively. According to both IAS and HIVdb, in the study period resistance to any class, nucleoside reverse inhibitor, non-nucleoside reverse inhibitor, and protease inhibitors (PIs) declined significantly. Integrase strand transfer inhibitor (INSTI) resistance declined significantly from 31% (36/116) to 20.8% (41/197) according to HIVdb but not to IAS. Divergent data were highlighted regarding the proportion of non-European patients carrying any, PI and INSTI resistance using IAS tables compared with the Stanford HIVdb algorithm, as the former failed to detect a decrease in resistance while the latter indicates a reduction of 1.6-, 5- and 1.8-fold resistance for such drug classes. In the multivariate analysis, the risk of resistance increased in patients with a larger number of treatment lines and higher viraemia and decreased in those starting therapy in the last biennium of the study. DISCUSSION A marked reduction in drug resistance was observed over 10 years, compatible with higher genetic barrier and potency of new antiretrovirals. Nonetheless, concerns remain for subjects with non-B subtypes when using mutation lists instead of interpretation systems because of the extensive polymorphism of the protease region.
Collapse
Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy.
| | - Marco Franzetti
- Infectious Diseases Unit, 'A. Manzoni' Hospital, Lecco, Italy
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Bianca Bruzzone
- Hygiene Unit, Policlinico San Martino Hospital, Genoa, Italy
| | - Simona Di Giambenedetto
- Institute of Clinical Infectious Diseases, Catholic University of the Sacred Heart of Rome, Rome, Italy
| | - Antonio Di Biagio
- Infectious Diseases Clinic, Department of Health Sciences, University of Genoa, San Martino Hospital-IRCCS, Genoa, Italy
| | - Sergio Lo Caputo
- Clinic of Infectious Diseases, University Hospital Policlinico, University of Bari, Bari, Italy
| | | | - Franco Maggiolo
- Clinic of Infectious Diseases, Ospedali Riuniti, Bergamo, Italy
| | - Saverio G Parisi
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Stefano Rusconi
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | | | - Claudia Balotta
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| |
Collapse
|
20
|
Hemmersbach-Miller M, Wood RP, Wolfe CR. Donor evaluation in the era of HIV-positive organ transplantation: The importance of the infectious diseases specialist. Am J Transplant 2020; 20:2589-2592. [PMID: 32301273 PMCID: PMC7540733 DOI: 10.1111/ajt.15921] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/25/2020] [Accepted: 03/31/2020] [Indexed: 01/25/2023]
Abstract
A 61-year-old female with well-controlled human immunodeficiency virus (HIV) and end-stage renal disease was on the kidney transplant waitlist awaiting an organ offer, including from HIV-positive donors through the HIV Organ Policy Equity (HOPE) Act. We present three different scenarios where HIV-positive donor offers were evaluated for this one recipient, discuss the donor evaluation process, explain where the infectious diseases provider fits in this scheme, and describe the challenges encountered by organ procurement organizations. This is the first case under the HOPE Act at our center where discovery of an HIV-specific issue led to a turndown of an organ offer.
Collapse
Affiliation(s)
- Marion Hemmersbach-Miller
- Division of Infectious Diseases, Duke University Medical Center. Durham, NC.,Duke Clinical Research Institute, Duke University, Durham, NC
| | | | - Cameron R. Wolfe
- Division of Infectious Diseases, Duke University Medical Center. Durham, NC
| |
Collapse
|
21
|
Marcelin AG, Grude M, Charpentier C, Bellecave P, Le Guen L, Pallier C, Raymond S, Mirand A, Bocket L, Fofana DB, Delaugerre C, Nguyen T, Montès B, Jeulin H, Mourez T, Fafi-Kremer S, Amiel C, Roussel C, Dina J, Trabaud MA, Le Guillou-Guillemette H, Vallet S, Signori-Schmuck A, Maillard A, Ferre V, Descamps D, Calvez V, Flandre P. Resistance to integrase inhibitors: a national study in HIV-1-infected treatment-naive and -experienced patients. J Antimicrob Chemother 2020; 74:1368-1375. [PMID: 30789205 DOI: 10.1093/jac/dkz021] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/26/2018] [Accepted: 01/02/2019] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES To describe integrase strand transfer inhibitor (INSTI) resistance profiles and factors associated with resistance in antiretroviral-naive and -experienced patients failing an INSTI-based regimen in clinical practice. METHODS Data were collected from patients failing an INSTI-containing regimen in a multicentre French study between 2014 and 2017. Failure was defined as two consecutive plasma viral loads (VL) >50 copies/mL. Reverse transcriptase, protease and integrase coding regions were sequenced at baseline and failure. INSTI resistance-associated mutations (RAMs) included in the Agence Nationale de Recherches sur le SIDA genotypic algorithm were investigated. RESULTS Among the 674 patients, 359 were failing on raltegravir, 154 on elvitegravir and 161 on dolutegravir therapy. Overall, 90% were experienced patients and 389 (58%) patients showed no INSTI RAMs at failure. The strongest factors associated with emergence of at least one INSTI mutation were high VL at failure (OR = 1.2 per 1 log10 copies/mL increase) and low genotypic sensitivity score (GSS) (OR = 0.08 for GSS ≥3 versus GSS = 0-0.5). Patients failing dolutegravir also had significantly fewer INSTI RAMs at failure than patients failing raltegravir (OR = 0.57, P = 0.02) or elvitegravir (OR = 0.45, P = 0.005). Among the 68 patients failing a first-line regimen, 11/41 (27%) patients on raltegravir, 7/18 (39%) on elvitegravir and 0/9 on dolutegravir had viruses with emergent INSTI RAMs at failure. CONCLUSIONS These results confirmed the robustness of dolutegravir regarding resistance selection in integrase in the case of virological failure in routine clinical care.
Collapse
Affiliation(s)
- Anne-Genevieve Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France
| | - Maxime Grude
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France
| | - Charlotte Charpentier
- INSERM, IAME, UMR 1137, F-75018 Paris, France; Université Paris Diderot, Sorbonne Paris Cité, F-75018 Paris, France; AP-HP, Hôpital Bichat, Laboratoire de Virologie, Paris, France
| | - Pantxika Bellecave
- CHU de Bordeaux, Laboratoire de Virologie, Université Bordeaux, CNRS UMR 5234, Bordeaux, France
| | - Laura Le Guen
- CHU de Nantes, Laboratoire de Virologie, Nantes, France
| | | | - Stéphanie Raymond
- INSERM U1043 Toulouse, F-31300 France and Laboratoire de Virologie, CHU Toulouse Purpan, Toulouse, France
| | | | | | - Djeneba Bocar Fofana
- Sorbonne Université, INSERM, Institut Pierre Louis, d'Epidémiologie et de Santé Publique (IPLESP), AP-HP, Hôpital Saint Antoine, Service de Virologie, Paris, France
| | | | - Thuy Nguyen
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France
| | | | - Hélène Jeulin
- Laboratoire de Virologie, CHRU de Nancy Brabois, Vandoeuvre-lès-Nancy, France
| | | | | | | | | | | | | | | | | | | | | | - Virginie Ferre
- CHU Nantes, Laboratoire de Virologie, CIC INSERM 143, Nantes, France
| | - Diane Descamps
- INSERM, IAME, UMR 1137, F-75018 Paris, France; Université Paris Diderot, Sorbonne Paris Cité, F-75018 Paris, France; AP-HP, Hôpital Bichat, Laboratoire de Virologie, Paris, France
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France
| | - Philippe Flandre
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France
| | | |
Collapse
|
22
|
Masoud S, Kamori D, Barabona G, Mahiti M, Sunguya B, Lyamuya E, Ueno T. Circulating HIV-1 Integrase Genotypes in Tanzania: Implication on the Introduction of Integrase Inhibitors-Based Antiretroviral Therapy Regimen. AIDS Res Hum Retroviruses 2020; 36:539-543. [PMID: 32126792 DOI: 10.1089/aid.2020.0021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Tanzania has recently adapted World Health Organization antiretroviral guidelines that include integrase strand transfer inhibitors (INSTIs) in the first-line regimen. However, there is lack of evidence on integrase (IN) gene polymorphisms in viral strains circulating in Tanzania. In this study, we characterize IN gene polymorphisms in viral strains circulating in Dar es Salaam, Tanzania, before introduction of INSTIs. Plasma viral RNAs were prepared from 158 HIV-1-infected subjects, including 111 treated, but viremic (INSTI-naïve), subjects. A part of the pol gene encompassing the IN-coding region was amplified and directly sequenced by the Sanger sequencing method. Subtype analysis revealed that subtypes A1, C, and D and intersubtype recombinants were 42%, 38%, 11%, and 9%, respectively. Although multiple subtypes cocirculate, the IN gene exhibited a relatively conserved amino acid sequence pattern with an average Shannon entropy score of 0.16. No major INSTI resistance mutations were found; however, accessory resistance mutations at positions T97A, E157Q, G163E/K, and 128A/T were detected in 5% of subjects.
Collapse
Affiliation(s)
- Salim Masoud
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Doreen Kamori
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Godfrey Barabona
- Division of Infection and Immunity, Joint Sciences Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Macdonald Mahiti
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Bruno Sunguya
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Eligius Lyamuya
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Takamasa Ueno
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Division of Infection and Immunity, Joint Sciences Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| |
Collapse
|
23
|
Molecular dynamic simulations to investigate the structural impact of known drug resistance mutations on HIV-1C Integrase-Dolutegravir binding. PLoS One 2020; 15:e0223464. [PMID: 32379830 PMCID: PMC7205217 DOI: 10.1371/journal.pone.0223464] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 04/21/2020] [Indexed: 12/18/2022] Open
Abstract
Resistance associated mutations (RAMs) threaten the long-term success of combination antiretroviral therapy (cART) outcomes for HIV-1 treatment. HIV-1 Integrase (IN) strand transfer inhibitors (INSTIs) have proven to be a viable option for highly specific HIV-1 therapy. The INSTI, Dolutegravir is recommended by the World Health Organization for use as first-line cART. This study aims to understand how RAMs affect the stability of IN, as well as the binding of the drug Dolutegravir to the catalytic pocket of the protein. A homology model of HIV-1 subtype C IN was successfully constructed and validated. The site directed mutator webserver was used to predict destabilizing and/or stabilizing effects of known RAMs while FoldX confirmed any changes in protein energy upon introduction of mutation. Also, interaction analysis was performed between neighbouring residues. Three mutations known to be associated with Raltegravir, Elvitegravir and Dolutegravir resistance were selected; E92Q, G140S and Y143R, for molecular dynamics simulations. The structural quality assessment indicated high reliability of the HIV-1C IN tetrameric structure, with more than 90% confidence in modelled regions. Change in free energy for the three mutants indicated different effects, while simulation analysis showed G140S to have the largest affect on protein stability and flexibility. This was further supported by weaker non-bonded pairwise interaction energy and binding free energy values between the drug DTG and E92Q, Y143R and G140S mutants suggesting reduced binding affinity, as indicated by interaction analysis in comparison to the WT. Our findings suggest the G140S mutant has the strongest effect on the HIV-1C IN protein structure and Dolutegravir binding. To the best of our knowledge, this is the first study that uses the consensus wild type HIV-1C IN sequence to build an accurate 3D model to understand the effect of three known mutations on DTG drug binding in a South Africa context.
Collapse
|
24
|
Obasa AE, Mikasi SG, Brado D, Cloete R, Singh K, Neogi U, Jacobs GB. Drug Resistance Mutations Against Protease, Reverse Transcriptase and Integrase Inhibitors in People Living With HIV-1 Receiving Boosted Protease Inhibitors in South Africa. Front Microbiol 2020; 11:438. [PMID: 32265875 PMCID: PMC7099763 DOI: 10.3389/fmicb.2020.00438] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/02/2020] [Indexed: 12/17/2022] Open
Abstract
The South African national combination antiretroviral therapy (cART) roll-out program started in 2006, with over 4.4 million people accessing treatment since it was first introduced. HIV-1 drug resistance can hamper the success of cART. This study determined the patterns of HIV-1 drug-resistance associated mutations (RAMs) in People Living with HIV-1 (PLHIV-1). Receiving first (for children below 3 years of age) and second-line (for adults) cART regimens in South Africa. During 2017 and 2018, 110 patients plasma samples were selected, 96 samples including those of 17 children and infants were successfully analyzed. All patients were receiving a boosted protease inhibitor (bPI) as part of their cART regimen. The viral sequences were analyzed for RAMs through genotypic resistance testing. We performed genotypic resistance testing (GRT) for Protease inhibitors (PIs), Reverse transcriptase inhibitors (RTIs) and Integrase strand transfer inhibitors (InSTIs). Viral sequences were subtyped using REGAv3 and COMET. Based on the PR/RT sequences, HIV-1 subtypes were classified as 95 (99%) HIV-1 subtype C (HIV-1C) while one sample as 02_AG. Integrase sequencing was successful for 89 sequences, and all the sequences were classified as HIV-1C (99%, 88/89) except one sequence classified CRF02_AG, as observed in PR/RT. Of the 96 PR/RT sequences analyzed, M184V/I (52/96; 54%) had the most frequent RAM nucleoside reverse transcriptase inhibitor (NRTI). The most frequent non-nucleoside reverse transcriptase inhibitor (NNRTI) RAM was K103N/S (40/96, 42%). Protease inhibitor (PI) RAMs M46I and V82A were present in 12 (13%) of the sequences analyzed. Among the InSTI major RAM two (2.2%) sequences have Y143R and T97A mutations while one sample had T66I. The accessory RAM E157Q was identified in two (2.2%). The data indicates that the majority of the patients failed on bPIs didn't have any mutation; therefore adherence could be major issue in these groups of individuals. We propose continued viral load monitoring for better management of infected PLHIV.
Collapse
Affiliation(s)
- Adetayo Emmanuel Obasa
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm University, Stockholm, Sweden
| | - Sello Given Mikasi
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Dominik Brado
- Division of Virology, Institute for Virology and Immunobiology, Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Kamlendra Singh
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm University, Stockholm, Sweden
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm University, Stockholm, Sweden
| | - Graeme Brendon Jacobs
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| |
Collapse
|
25
|
Onoriode Digban T, Chucks Iweriebor B, Chikwelu Obi L, Nwodo U, Ifeanyi Okoh A. Analyses of HIV-1 integrase gene sequences among treatment-naive patients in the Eastern Cape, South Africa. J Med Virol 2020; 92:1165-1172. [PMID: 31889319 DOI: 10.1002/jmv.25661] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/21/2019] [Indexed: 01/11/2023]
Abstract
Drug resistance has been recognized in all available therapeutic class of medications for the management of human immunodeficiency virus-1 (HIV-1) infected patients. This makes the continuous study of HIV drug resistance and new treatment options pertinent to patients and researchers globally. The aim of this study is to analyze the complete HIV-1 integrase gene for the possible occurrence of resistance mutations or polymorphisms. We performed genetic analyses on 48 treatment-naive HIV-1-infected patients using nested polymerase chain reaction. Integrase drug-related resistance mutation (DRMs) analysis was performed on all generated sequences according to Stanford HIV drug interpretation program and the International AIDS Society-USA guidelines while phylogenetic analysis was inferred using MEGA 6. The study revealed no major resistance-associated mutation. However, E157Q (2.1%), L74M/I (4.2%), and P142T (2.1%) were the observed accessory and polymorphic mutations. Naturally occurring polymorphism observed were E11D, K14R, D25E, V31I, M50I, V72I, P90T, F100Y, L101I, T124A, T125A, K136Q, D167E, V201I, L234I, A265V, A269K, D278A, and S283G. Phylogenetic analysis delineated all the sequences as HIV-1 subtype C. The study revealed the absence of major integrase inhibitors associated resistance mutations in a setting where integrase inhibitor is administered as salvage therapy in patients developing resistance to first and second-line antiretroviral treatment. However minor and natural polymorphisms were observed and thus may influence the outcome of each treatment regimen. However, additional studies are required to precisely evaluate the impact of these mutations on integrase inhibitors in the Eastern Cape of South Africa.
Collapse
Affiliation(s)
- Tennison Onoriode Digban
- South Africa Medical Research Council and Water Quality Monitoring Centre, University of Fort Hare, Alice, Eastern Cape, South Africa.,Applied Environmental and Microbiology Research Group, University of Fort Hare, Alice, Eastern Cape, South Africa.,Department of Microbiology and Biochemistry, University of Fort Hare, Alice, Eastern Cape, South Africa
| | - Benson Chucks Iweriebor
- School of Science and Technology, Sefako Makgatho Health Sciences University, Ga-Rankuwa, Pretoria, South Africa
| | - Larry Chikwelu Obi
- School of Science and Technology, Sefako Makgatho Health Sciences University, Ga-Rankuwa, Pretoria, South Africa
| | - Uchechuwku Nwodo
- South Africa Medical Research Council and Water Quality Monitoring Centre, University of Fort Hare, Alice, Eastern Cape, South Africa.,Applied Environmental and Microbiology Research Group, University of Fort Hare, Alice, Eastern Cape, South Africa.,Department of Microbiology and Biochemistry, University of Fort Hare, Alice, Eastern Cape, South Africa
| | - Anthony Ifeanyi Okoh
- South Africa Medical Research Council and Water Quality Monitoring Centre, University of Fort Hare, Alice, Eastern Cape, South Africa.,Applied Environmental and Microbiology Research Group, University of Fort Hare, Alice, Eastern Cape, South Africa.,Department of Microbiology and Biochemistry, University of Fort Hare, Alice, Eastern Cape, South Africa
| |
Collapse
|
26
|
Santerre M, Wang Y, Arjona S, Allen C, Sawaya BE. Differential Contribution of HIV-1 Subtypes B and C to Neurological Disorders: Mechanisms and Possible Treatments. AIDS Rev 2019; 21:76-83. [PMID: 31332398 DOI: 10.24875/aidsrev.19000051] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
With the introduction of combinatory antiretroviral therapy, patients infected with human immunodeficiency virus type 1 (HIV-1) can live much longer than before. However, the identification of HIV-associated neurocognitive disorder (HAND), especially HIV-associated dementia in 15-20% of patients infected with HIV-1, indicates additional complexity. These disorders turn out to be subtype dependent. Recently, many studies are ongoing trying to understand how the virus induces neuronal injury which could lead to neurological dysfunction. Most of these studies are focusing on the HIV-1 release of proteins such as Tat. However, the exact role of these proteins and their involvement in neuronal degeneration remains unidentified; this is especially true since viral proteins from different HIV-1 subtypes differ in their ability to cause neuronal damage. This review describes the role of different HIV-1 subtypes, identifies probable pathways involved in neuronal damage, the contribution of different HIV-1 subtypes to the progression of HAND, and potential treatments for HAND.
Collapse
Affiliation(s)
- Maryline Santerre
- Molecular Studies of Neurodegenerative Diseases Lab, FELS Institute for Cancer Research and Molecular Biology, Philadelphia, Pennsylvania, USA
| | - Ying Wang
- Molecular Studies of Neurodegenerative Diseases Lab, FELS Institute for Cancer Research and Molecular Biology, Philadelphia, Pennsylvania, USA
| | - Sterling Arjona
- Molecular Studies of Neurodegenerative Diseases Lab, FELS Institute for Cancer Research and Molecular Biology, Philadelphia, Pennsylvania, USA
| | - Charles Allen
- Molecular Studies of Neurodegenerative Diseases Lab, FELS Institute for Cancer Research and Molecular Biology, Philadelphia, Pennsylvania, USA
| | - Bassel E Sawaya
- Department of Neurology, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, USA
| |
Collapse
|
27
|
Achieng L, Riedel DJ. Dolutegravir Resistance and Failure in a Kenyan Patient. J Infect Dis 2019; 219:165-167. [PMID: 30165703 DOI: 10.1093/infdis/jiy436] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Loice Achieng
- Department of Clinical Medicine and Therapeutics, University of Nairobi, Kenya
| | - David J Riedel
- Institute of Human Virology and Division of Infectious Diseases, University of Maryland School of Medicine, Baltimore
| |
Collapse
|
28
|
Zamora FJ, Dowers E, Yasin F, Ogbuagu O. Dolutegravir And Lamivudine Combination For The Treatment Of HIV-1 Infection. HIV AIDS-RESEARCH AND PALLIATIVE CARE 2019; 11:255-263. [PMID: 31749636 PMCID: PMC6817767 DOI: 10.2147/hiv.s216067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 09/12/2019] [Indexed: 12/11/2022]
Abstract
There have been remarkable advances in drug development for the treatment of HIV-1 infection. From the co-formulation of combination antiretroviral therapy (cART) into single-tablet regimens to the development of long-acting antiretroviral (ARV) drug formulations, the treatment of HIV has and will become much more tolerable and less complicated for patients. In addition, and appropriately, there is a focus on reducing short- and long-term toxicities of treatment while maintaining robust efficacy. One of such approaches includes 2-drug regimen constructs that contain and retain effective ARV compounds while excluding components that have relatively unfavorable toxicity profiles. The first-ever 2-drug regimen approved for the treatment of HIV-1 infection for treatment-naive people living with HIV (PLWH), consisting of the integrase inhibitor dolutegravir (DTG) and the nucleoside reverse transcriptase inhibitor (NRTI) lamivudine (3TC), is reviewed in this paper. The chemical composition and properties, pharmacokinetic and pharmacodynamics profile, and clinical trial data on efficacy and safety of DTG/3TC are presented. An expert opinion aims to highlight important considerations for the use of DTG/3TC in the context of existing and emerging ARV options.
Collapse
Affiliation(s)
- Francis J Zamora
- Department of Pharmacy Services, Broward Health Medical Center, Fort Lauderdale, FL, USA.,Department of Pharmacy Services, Yale-New Haven Hospital, New Haven, CT, USA
| | - Ellen Dowers
- Department of Pharmacy Services, Yale-New Haven Hospital, New Haven, CT, USA
| | - Faiza Yasin
- Section of Infectious Diseases, Yale AIDS Program, Yale University School of Medicine, New Haven, CT, USA
| | - Onyema Ogbuagu
- Section of Infectious Diseases, Yale AIDS Program, Yale University School of Medicine, New Haven, CT, USA
| |
Collapse
|
29
|
Veldkamp PJ, Mellors JW, Halvas EK. The Argument Against Testing for INSTI Resistance in Treatment Naive Patients. Clin Infect Dis 2019; 66:1820-1821. [PMID: 29324987 DOI: 10.1093/cid/ciy015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - John W Mellors
- University of Pittsburgh School of Medicine, Pennsylvania
| | - Elias K Halvas
- University of Pittsburgh School of Medicine, Pennsylvania
| |
Collapse
|
30
|
Abstract
Approximately 20% of people with HIV in the United States prescribed antiretroviral therapy are not virally suppressed. Thus, optimal management of virologic failure has a critical role in the ability to improve viral suppression rates to improve long-term health outcomes for those infected and to achieve epidemic control. This article discusses the causes of virologic failure, the use of resistance testing to guide management after failure, interpretation and relevance of HIV drug resistance patterns, considerations for selection of second-line and salvage therapies, and management of virologic failure in special populations.
Collapse
Affiliation(s)
- Suzanne M McCluskey
- Division of Infectious Diseases, Harvard Medical School, Massachusetts General Hospital, 55 Fruit Street, GRJ5, Boston, MA 02114, USA.
| | - Mark J Siedner
- Division of Infectious Diseases, Harvard Medical School, Massachusetts General Hospital, 55 Fruit Street, GRJ5, Boston, MA 02114, USA
| | - Vincent C Marconi
- Division of Infectious Diseases, Department of Global Health, Emory University School of Medicine, Rollins School of Public Health, Health Sciences Research Building, 1760 Haygood Dr NE, Room W325, Atlanta, GA 30322, USA
| |
Collapse
|
31
|
Scutari R, Alteri C, Vicenti I, Di Carlo D, Zuccaro V, Incardona F, Borghi V, Bezenchek A, Andreoni M, Antinori A, Perno CF, Cascio A, De Luca A, Zazzi M, Santoro MM. Evaluation of HIV-1 integrase resistance emergence and evolution in patients treated with integrase inhibitors. J Glob Antimicrob Resist 2019; 20:163-169. [PMID: 31330378 DOI: 10.1016/j.jgar.2019.07.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/26/2019] [Accepted: 07/12/2019] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVES This study evaluated the emergence of mutations associated with integrase strand transfer inhibitors (INSTI) resistance (INSTI-RMs) and the integrase evolution in human immunodeficiency virus type 1 (HIV-1) infected patients treated with this drug class. METHODS The emergence of INSTI-RMs and integrase evolution (estimated as genetic distance between integrase sequences under INSTI treatment and before INSTI treatment) were evaluated in 107 INSTI-naïve patients (19 drug-naïve and 88 drug-experienced) with two plasma genotypic resistance tests: one before INSTI treatment and one under INSTI treatment. A logistic regression analysis was performed to evaluate factors associated with the integrase evolution under INSTI treatment. RESULTS The patients were mainly infected by B subtype (72.0%). Eighty-seven patients were treated with raltegravir, 13 with dolutegravir and seven with elvitegravir. Before INSTI treatment one patient harboured the major INSTI-RM R263K and three patients the accessory INSTI-RMs T97A. Under INSTI treatment the emergence of ≥1 INSTI-RM was found in 39 (36.4%) patients. The major INSTI-RMs that more frequently emerged were: N155H (17.8%), G140S (8.4%), Y143R (7.5%), Q148H (6.5%), and Y143C (4.7%). Concerning integrase evolution, a higher genetic distance was found in patients with ≥1 INSTI-RM compared with those without emergence of resistance (0.024 [0.012-0.036] vs. 0.015 [0.009-0.024], P=0.018). This higher integrase evolution was significantly associated with a longer duration of HIV-1 infection, a higher number of past regimens and non-B subtypes. CONCLUSIONS These findings confirm that major INSTI-RMs very rarely occur in INSTI-naïve patients. Under INSTI treatment, selection of drug-resistance follows the typical drug-resistance pathways; a higher evolution characterises integrase sequences developing drug-resistance compared with those without any resistance.
Collapse
Affiliation(s)
| | - Claudia Alteri
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | | | - Domenico Di Carlo
- University of Milan, Paediatric Clinical Research Center "Romeo and Enrica Invernizzi", Milan, Italy
| | | | | | - Vanni Borghi
- Infectious Diseases Clinics, Azienda Ospedaliero-Universitaria Policlinico di Modena, Modena, Italy
| | | | | | - Andrea Antinori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | | | | | | | | | | | | |
Collapse
|
32
|
Alaoui N, El Alaoui MA, El Annaz H, Farissi FZ, Alaoui AS, El Fahime E, Mrani S. HIV-1 Integrase Resistance among Highly Antiretroviral Experienced Patients from Morocco. Intervirology 2019; 62:65-71. [PMID: 31307042 DOI: 10.1159/000501016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 05/14/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND We aimed to analyze for the first time in Morocco the integrase (IN) sequence variability among highly experienced HIV-1-infected patients with no prior IN strand transfer inhibitor (INSTI) exposure who failed on reverse transcriptase inhibitors and protease inhibitors. METHODS The HIV-1 IN region was sequenced from plasma samples of all 78 recruited patients. The amino acid IN sequences were HIV-1 subtyped and screened for the presence of polymorphisms against the HxB2 clade B consensus sequence by the geno2pheno subtyping tool and interpreted for drug resistance according to the Stanford algorithm. RESULTS The viral subtypes were subtype B (88.4%), CRF02_AG (8.9%), CRF01_AE (1.28%), and subtype C (1.28%). The major INSTI resistance mutations at positions 66, 92, 118, 138, 140, 143, 147, 148, 155, and 263 were absent, while two accessory mutations, L74M/I, known to have no clinical impact to INSTIs in the absence of the major resistance mutations, were detected in three samples (3.84%; two CRF02_AG and one CRF01_AE). Others specific substitutions with an uncertain role on the HIV-1 susceptibility to INSTIs at positions 72, 101, 119, 124, 156, 165, 193, 201, 203, 206, 230, 232, and 249 were found to be relatively common. CONCLUSION This study demonstrated that INSTIs should be an excellent alternative for salvage therapy in highly experienced patients with multidrug resistant viruses in Morocco.
Collapse
Affiliation(s)
- Najwa Alaoui
- Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco, .,Research Team in Molecular Virology and Oncobiology, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco,
| | - Moulay Abdelaziz El Alaoui
- Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco.,Molecular Biology and Functional Genomics Platform, National Center for Scientific and Technical Research, Rabat, Morocco.,Laboratory of Genetics and Biometry, Faculty of Sciences, Ibn Tofail University, Kenitra, Morocco
| | - Hicham El Annaz
- Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco.,Research Team in Molecular Virology and Oncobiology, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Fatima Zahra Farissi
- Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco.,Research Team in Molecular Virology and Oncobiology, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Amine Sanaâ Alaoui
- Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco.,Molecular Biology and Functional Genomics Platform, National Center for Scientific and Technical Research, Rabat, Morocco
| | - Elmostapha El Fahime
- Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco.,Molecular Biology and Functional Genomics Platform, National Center for Scientific and Technical Research, Rabat, Morocco
| | - Saad Mrani
- Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco.,Research Team in Molecular Virology and Oncobiology, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco.,National Reference Laboratory, Mohammed VI University of Science, Casablanca, Morocco
| |
Collapse
|
33
|
Resistance Analysis of Bictegravir-Emtricitabine-Tenofovir Alafenamide in HIV-1 Treatment-Naive Patients through 48 Weeks. Antimicrob Agents Chemother 2019; 63:AAC.02533-18. [PMID: 30803969 DOI: 10.1128/aac.02533-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 02/17/2019] [Indexed: 11/20/2022] Open
Abstract
In clinical studies GS-US-380-1489 (study 1489) and GS-US-380-1490 (study 1490), bictegravir-emtricitabine-tenofovir alafenamide (B-F-TAF), dolutegravir-abacavir-lamivudine (DTG-ABC-3TC), and dolutegravir plus emtricitabine-tenofovir alafenamide (DTG+F-TAF) treatment achieved high rates of virologic suppression in HIV-1 treatment-naive participants through week 48. Preexisting primary drug resistance was present at levels of 1.3% integrase strand transfer inhibitor resistance (INSTI-R), 2.7% nucleoside reverse transcriptase inhibitor resistance (NRTI-R), 14.1% nonnucleoside reverse transcriptase inhibitor resistance (NNRTI-R), and 3.5% protease inhibitor resistance (PI-R) in the 1,274 participants from these studies. These mutations did not affect treatment outcomes. Resistance analyses in 13 virologic failures found no emergent resistance to study drugs.
Collapse
|
34
|
Alvarez M, Casas P, de Salazar A, Chueca N, Guerrero-Beltran C, Rodríguez C, Imaz A, Espinosa N, García-Bujalance S, Pérez-Elías MJ, García-Alvarez M, Iribarren JA, Santos J, Dalmau D, Aguilera A, Vinuesa D, Gutiérrez F, Piérola B, Molina JM, Peraire J, Portilla I, Gómez-Sirvent JL, Olalla J, Galera C, Blanco JR, Riera M, García-Fraile L, Navarro G, Curran A, Poveda E, García F, Moreno S, Jarrín I, Dalmau D, Navarro ML, González MI, Blanco JL, Garcia F, Rubio R, Iribarren JA, Gutiérrez F, Vidal F, Berenguer J, González J, Alejos B, Hernando V, Moreno C, Iniesta C, Sousa LMG, Perez NS, Muñoz-Fernández MÁ, García-Merino IM, Fernández IC, Rico CG, de la Fuente JG, Concejo PP. Surveillance of transmitted drug resistance to integrase inhibitors in Spain: implications for clinical practice. J Antimicrob Chemother 2019; 74:1693-1700. [DOI: 10.1093/jac/dkz067] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 01/17/2019] [Accepted: 01/24/2019] [Indexed: 12/20/2022] Open
Affiliation(s)
- Marta Alvarez
- Unidad de Microbiología Clínica, Hospital Universitario San Cecilio, Granada, Instituto de Investigacion Ibs., Granada, Spain
| | - Paz Casas
- Unidad de Microbiología Clínica, Hospital Universitario San Cecilio, Granada, Instituto de Investigacion Ibs., Granada, Spain
| | - Adolfo de Salazar
- Unidad de Microbiología Clínica, Hospital Universitario San Cecilio, Granada, Instituto de Investigacion Ibs., Granada, Spain
| | - Natalia Chueca
- Unidad de Microbiología Clínica, Hospital Universitario San Cecilio, Granada, Instituto de Investigacion Ibs., Granada, Spain
| | - Carlos Guerrero-Beltran
- Unidad de Microbiología Clínica, Hospital Universitario San Cecilio, Granada, Instituto de Investigacion Ibs., Granada, Spain
| | | | - Arkaitz Imaz
- Unidad de VIH e ITS, Departamento de Enfermedades Infecciosas, Hospital Universitari de Bellvitge-IDIBELL, L’Hospitalet de Llobregat, Barcelona, Spain
| | - Nuria Espinosa
- Unidad de Enfermedades Infecciosas, Hospital Virgen del Rocio, Sevilla, Spain
| | | | | | - Mónica García-Alvarez
- Unidad de Microbiología Clínica, Hospital Universitario Doce de Octubre, Madrid, Spain
| | - Jose Antonio Iribarren
- Unidad de Enfermedades Infecciosas, Hospital Universitario Donostia, Instituto BioDonostia, Donostia, Spain
| | - Jesús Santos
- Unidad de Enfermedades Infecciosas, Hospital Universitario Virgen de la Victoria, Málaga, Spain
| | - David Dalmau
- Unidad de Enfermedades Infecciosas, Hospital Universitario Mutua Terrasa, Terrasa, Spain
| | - Antonio Aguilera
- Servicio y Departamento de Microbiología, Complejo Hospitalario Universitario de Santiago y Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - David Vinuesa
- Unidad de Enfermedades Infecciosas, Hospital Universitario, Universitario San Cecilio, Granada, Spain
| | - Félix Gutiérrez
- Unidad de Enfermedades Infecciosas, Hospital Universitario de Elche & Universidad Miguel Hernández, Alicante, Spain
| | - Beatriz Piérola
- Unidad de Enfermedades Infecciosas, Complejo Hospitalario de Navarra, Pamplona, Spain
| | - José Miguel Molina
- Unidad de Microbiología Clínica, Hospital Universitario La Fe, Valencia, Spain
| | - Joaquim Peraire
- Unidad de Enfermedades Infecciosas, Hospital Universitari de Tarragona Joan XXIII, IISPV, Universitat Rovira i Virgili, Tarragona, Spain
| | - Irene Portilla
- Unidad de Enfermedades Infecciosas, Hospital Universitario Alicante, Alicante, Spain
| | - Juan Luis Gómez-Sirvent
- Unidad de Enfermedades Infecciosas, Hospital Universitario de Canarias, Santa Cruz de Tenerife, Spain
| | - Julián Olalla
- Unidad de Enfermedades Infecciosas, Hospital Costa del Sol, Marbella, Spain
| | - Carlos Galera
- Unidad de Enfermedades Infecciosas, Hospital Universitario Virgen de la Arrixaca, Murcia, Spain
| | - José Ramón Blanco
- Unidad de Enfermedades Infecciosas, Hospital Universitario San Pedro, Logroño, Spain
| | - Melchor Riera
- Unidad de Enfermedades Infecciosas, Hospital Universitario Son Espases, Palma de Mallorca, Spain
| | - Lucio García-Fraile
- Unidad de Enfermedades Infecciosas, Hospital Universitario La Princesa, Madrid, Spain
| | - Gemma Navarro
- Unidad de Enfermedades Infecciosas, Hospital Universitario Parc Taulí, Sabadell, Spain
| | - Adrían Curran
- Servicio de Enfermedades Infecciosas, Hospital Universitario Vall d´Hebron, Barcelona, Spain
| | - Eva Poveda
- Group of Virology and Pathogenesis, Galicia Sur Health Research Institute (IIS Galicia Sur)-Complexo Hospitalario Universitario de Vigo, SERGAS-UVigo, Spain
| | - Federico García
- Unidad de Microbiología Clínica, Hospital Universitario San Cecilio, Granada, Instituto de Investigacion Ibs., Granada, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Integrase Resistance-Associated Mutations on Raltegravir Failure in Western India: A Preliminary Analysis. J Acquir Immune Defic Syndr 2019; 77:e42-e45. [PMID: 29315113 DOI: 10.1097/qai.0000000000001625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
36
|
Modica S, Rossetti B, Lombardi F, Lagi F, Maffeo M, D'Autilia R, Pecorari M, Vicenti I, Bruzzone B, Magnani G, Paolucci S, Francisci D, Penco G, Sacchini D, Zazzi M, De Luca A, Di Biagio A. Prevalence and determinants of resistance mutations in HIV-1-infected patients exposed to integrase inhibitors in a large Italian cohort. HIV Med 2018; 20:137-146. [PMID: 30461149 DOI: 10.1111/hiv.12692] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2018] [Indexed: 12/21/2022]
Abstract
OBJECTIVES The aim of the study was to analyse the prevalence of integrase resistance mutations in integrase strand transfer inhibitor (INSTI)-experienced HIV-1-infected patients and its predictors. METHODS We selected HIV-1 integrase sequences from the Antiviral Response Cohort Analysis (ARCA) database, derived from INSTI-experienced patients between 2008 and 2017. Differences in the prevalence of resistance to raltegravir (RAL), elvitegravir (EVG) and dolutegravir (DTG) were assessed by χ2 test and predictors of resistance were analysed by logistic regression. RESULTS We included 462 genotypes from INSTI-exposed individuals: 356 'INSTI-failing' patients and 106 'previously INSTI-exposed' patients (obtained a median of 42 weeks after INSTI discontinuation [interquartile range (IQR) 17-110 weeks]). Overall, at least low-level resistance (LLR) to any INSTI (Stanford 8.5 algorithm) was detected in 198 (42.9%) cases. The most frequent INSTI resistance mutation was N155H, followed by Q148H/K/R, G140A/C/S, E138A/K/T and Y143C/H/R. Y143R and E138A were more prevalent in viral subtype B versus non-B [5.2 versus 1.5%, respectively (P = 0.04), and 3.1 versus 0%, respectively (P = 0.02)]. Overall, the Q148H/K/R plus G140A/C/S and/or E138A/K/T pattern, defining an intermediate level of resistance to DTG, was detected in 70 (15%) cases. Independent predictors of at least LLR to any INSTI were current use versus past use of INSTIs, a lower genotypic sensitivity score (GSS) for contemporary antiretroviral drugs used, and having an integrase sequence obtained in calendar year 2016 as compared to 2008-2009. CONCLUSIONS The results support integrase resistance testing in INSTI-experienced patients. Emergence of INSTI resistance is facilitated by the reduced genetic barrier of the regimen as a consequence of resistance to companion drugs. However, INSTI resistance may become undetectable by standard population sequencing upon INSTI discontinuation.
Collapse
Affiliation(s)
- S Modica
- Infectious Diseases Unit, Siena University Hospital, Siena, Italy.,Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - B Rossetti
- Infectious Diseases Unit, Siena University Hospital, Siena, Italy
| | - F Lombardi
- Institute of Clinical Infectious Diseases, Catholic University of the Sacred Heart, Rome, Italy
| | - F Lagi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - M Maffeo
- Infectious Diseases Unit, Siena University Hospital, Siena, Italy.,Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - R D'Autilia
- Department of Mathematics, University of Roma Tre, Rome, Italy
| | - M Pecorari
- Unit of Microbiology and Virology, Modena University Hospital, Modena, Italy
| | - I Vicenti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - B Bruzzone
- Hygiene Unit, Policlinico San Martino Hospital, Genoa, Italy
| | - G Magnani
- Department of Infectious Diseases, S. Maria Nuova IRCCS Hospital, Reggio Emilia, Italy
| | - S Paolucci
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS San Matteo Hospital Foundation, Pavia, Italy
| | - D Francisci
- Infectious Diseases Clinic, Perugia University Hospital, Perugia, Italy
| | - G Penco
- Department of Infectious Diseases, Galliera Hospital, Genoa, Italy
| | - D Sacchini
- Clinic of Infectious Diseases, 'Guglielmo da Saliceto' Hospital, Piacenza, Italy
| | - M Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - A De Luca
- Infectious Diseases Unit, Siena University Hospital, Siena, Italy.,Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - A Di Biagio
- Infectious Diseases Clinic, Policlinico San Martino Hospital, Genoa, Italy
| |
Collapse
|
37
|
[HIV-1 integrase inhibitor resistance among treatment naïve patients in Gran Canaria, 2017]. REVISTA ESPANOLA DE QUIMIOTERAPIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE QUIMIOTERAPIA 2018; 31:459-460. [PMID: 30221902 PMCID: PMC6194871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
38
|
Marino-Merlo F, Macchi B, Armenia D, Bellocchi MC, Ceccherini-Silberstein F, Mastino A, Grelli S. Focus on recently developed assays for detection of resistance/sensitivity to reverse transcriptase inhibitors. Appl Microbiol Biotechnol 2018; 102:9925-9936. [PMID: 30269214 DOI: 10.1007/s00253-018-9390-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/07/2018] [Accepted: 09/09/2018] [Indexed: 12/23/2022]
Abstract
The biology of HIV is rather complex due to high rate of replication, frequent recombination, and introduction of mutations. This gives rise to a number of distinct variants referred as quasispecies. In addition, the latency within reservoir allows the periodic reactivation of virus replication. The rapid replication of HIV allows immune response escape and establishment of resistance to therapy that can be acquired through drug selection and/or transmitted among individuals. This prompted, over the years, the development of a range of assays aimed to determine drug resistance and sensitivity, to be used both in clinical practice and in antiviral research. Reverse transcriptase (RT) inhibitors have an eminent place among the anti-HIV drugs, being constantly present from the beginning until today in the most commonly used antiviral regimens. This mini-review seeks to provide an up-to-date overview of recent efforts in developing even more reliable and simple methods, of both genotypic and phenotypic types, for specifically detecting drug resistance and sensitivity to RT inhibitors.
Collapse
Affiliation(s)
| | - Beatrice Macchi
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Daniele Armenia
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy
| | | | | | - Antonio Mastino
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Via F. Stagno d'Alcontres 31, 98166, Messina, Italy. .,The Institute of Translational Pharmacology, CNR, Rome, Italy.
| | - Sandro Grelli
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy
| |
Collapse
|
39
|
Fulcher JA, Du Y, Zhang TH, Sun R, Landovitz RJ. Emergence of Integrase Resistance Mutations During Initial Therapy Containing Dolutegravir. Clin Infect Dis 2018; 67:791-794. [PMID: 29933437 PMCID: PMC6093998 DOI: 10.1093/cid/ciy228] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/20/2018] [Indexed: 01/09/2023] Open
Abstract
Dolutegravir (DTG) is a preferred drug for initial treatment of human immunodeficiency virus type 1 infection. We present next-generation sequencing analysis of integrase genotypes during a period of virologic failure in a treatment-naive man who initiated tenofovir disoproxil fumarate/emtricitabine plus DTG.
Collapse
Affiliation(s)
- Jennifer A Fulcher
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles (UCLA)
- VA Greater Los Angeles Healthcare System
| | - Yushen Du
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA
| | - Tian-hao Zhang
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA
| | - Ren Sun
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA
| | - Raphael J Landovitz
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles (UCLA)
- Center for AIDS Research and Education, Los Angeles, California
| |
Collapse
|
40
|
Saag MS, Benson CA, Gandhi RT, Hoy JF, Landovitz RJ, Mugavero MJ, Sax PE, Smith DM, Thompson MA, Buchbinder SP, Del Rio C, Eron JJ, Fätkenheuer G, Günthard HF, Molina JM, Jacobsen DM, Volberding PA. Antiretroviral Drugs for Treatment and Prevention of HIV Infection in Adults: 2018 Recommendations of the International Antiviral Society-USA Panel. JAMA 2018; 320:379-396. [PMID: 30043070 PMCID: PMC6415748 DOI: 10.1001/jama.2018.8431] [Citation(s) in RCA: 440] [Impact Index Per Article: 73.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Importance Antiretroviral therapy (ART) is the cornerstone of prevention and management of HIV infection. Objective To evaluate new data and treatments and incorporate this information into updated recommendations for initiating therapy, monitoring individuals starting therapy, changing regimens, and preventing HIV infection for individuals at risk. Evidence Review New evidence collected since the International Antiviral Society-USA 2016 recommendations via monthly PubMed and EMBASE literature searches up to April 2018; data presented at peer-reviewed scientific conferences. A volunteer panel of experts in HIV research and patient care considered these data and updated previous recommendations. Findings ART is recommended for virtually all HIV-infected individuals, as soon as possible after HIV diagnosis. Immediate initiation (eg, rapid start), if clinically appropriate, requires adequate staffing, specialized services, and careful selection of medical therapy. An integrase strand transfer inhibitor (InSTI) plus 2 nucleoside reverse transcriptase inhibitors (NRTIs) is generally recommended for initial therapy, with unique patient circumstances (eg, concomitant diseases and conditions, potential for pregnancy, cost) guiding the treatment choice. CD4 cell count, HIV RNA level, genotype, and other laboratory tests for general health and co-infections are recommended at specified points before and during ART. If a regimen switch is indicated, treatment history, tolerability, adherence, and drug resistance history should first be assessed; 2 or 3 active drugs are recommended for a new regimen. HIV testing is recommended at least once for anyone who has ever been sexually active and more often for individuals at ongoing risk for infection. Preexposure prophylaxis with tenofovir disoproxil fumarate/emtricitabine and appropriate monitoring is recommended for individuals at risk for HIV. Conclusions and Relevance Advances in HIV prevention and treatment with antiretroviral drugs continue to improve clinical management and outcomes for individuals at risk for and living with HIV.
Collapse
Affiliation(s)
| | | | - Rajesh T Gandhi
- Massachusetts General Hospital and Harvard Medical School, Boston
| | - Jennifer F Hoy
- The Alfred Hospital and Monash University, Melbourne, Australia
| | | | | | - Paul E Sax
- Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts
| | | | | | - Susan P Buchbinder
- San Francisco Department of Public Health and University of California San Francisco
| | - Carlos Del Rio
- Emory University Rollins School of Public Health and School of Medicine, Atlanta, Georgia
| | - Joseph J Eron
- University of North Carolina at Chapel Hill School of Medicine
| | - Gerd Fätkenheuer
- University Hospital of Cologne, Department I of Internal Medicine, Cologne, Germany, and German Center for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
| | - Huldrych F Günthard
- University Hospital Zurich and Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | | | | |
Collapse
|
41
|
De Francesco MA, Izzo I, Properzi M, Gargiulo F, Caccuri F, Quiros-Roldan E, Castelli F, Caruso A, Focà E. Prevalence of Integrase Strand Transfer Inhibitors Resistance Mutations in Integrase Strand Transfer Inhibitors-Naive and -Experienced HIV-1 Infected Patients: A Single Center Experience. AIDS Res Hum Retroviruses 2018; 34:570-574. [PMID: 29631420 DOI: 10.1089/aid.2018.0006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Integrase strand transfer inhibitor (InSTI) resistance rates are low. However, genotypic resistance test (GRT) is not routinely performed in many centers. The aim of this study is to evaluate the prevalence of InSTI-related mutations in our large cohort. We examined all integrase GRTs performed as part of routine clinical practice at Spedali Civili General Hospital, University of Brescia from 2011 to 2016. Analysis was performed through the Stanford HIV Drug Resistance Database. A total of 341 patients were included. Genotypic resistance assays were performed in naive (48), ART-experienced but InSTI-naive (114), and both ART-experienced/InSTI-experienced (179) patients. No major resistance-associated mutations (RAMs) were detected in patients never exposed to InSTIs. Of 179 samples from patients exposed to InSTIs (mostly to raltegravir [RAL]), the overall prevalence of major RAMs was 11.7%. Among them, 10 harbored N155H, 4 Q148H, 2 Q148R, 2 Y143C/S, and 2 T66A/I/T, respectively. A novel mutation at a recognized resistance site (E92K) was identified in one RAL-experienced patient. The overall prevalence of InSTI mutations in our cohort was low, particularly in naive patients indicating no transmitted RAMs, although in InSTIs-experienced patients the rate of RAMs was high (11.7%). We support an implementation of surveillance of InSTI resistance.
Collapse
Affiliation(s)
- Maria Antonia De Francesco
- Department of Molecular and Translational Medicine, Institute of Microbiology, University of Brescia, Brescia, Italy
| | - Ilaria Izzo
- University Department of Infectious and Tropical Diseases, University of Brescia and Spedali Civili General Hospital, Brescia, Italy
| | - Martina Properzi
- University Department of Infectious and Tropical Diseases, University of Brescia and Spedali Civili General Hospital, Brescia, Italy
| | - Franco Gargiulo
- Department of Molecular and Translational Medicine, Institute of Microbiology, University of Brescia, Brescia, Italy
| | - Francesca Caccuri
- Department of Molecular and Translational Medicine, Institute of Microbiology, University of Brescia, Brescia, Italy
| | - Eugenia Quiros-Roldan
- University Department of Infectious and Tropical Diseases, University of Brescia and Spedali Civili General Hospital, Brescia, Italy
| | - Francesco Castelli
- University Department of Infectious and Tropical Diseases, University of Brescia and Spedali Civili General Hospital, Brescia, Italy
| | - Arnaldo Caruso
- Department of Molecular and Translational Medicine, Institute of Microbiology, University of Brescia, Brescia, Italy
| | - Emanuele Focà
- University Department of Infectious and Tropical Diseases, University of Brescia and Spedali Civili General Hospital, Brescia, Italy
| |
Collapse
|
42
|
Rusconi S, Adorni F, Tau P, Borghi V, Pecorari M, Maserati R, Francisci D, Monno L, Punzi G, Meraviglia P, Paolucci S, Di Biagio A, Bruzzone B, Mancon A, Micheli V, Zazzi M. Dolutegravir (DTG)-containing regimens after receiving raltegravir (RAL) or elvitegravir (EVG): Durability and virological response in a large Italian HIV drug resistance network (ARCA). J Clin Virol 2018; 105:112-117. [PMID: 29957545 DOI: 10.1016/j.jcv.2018.06.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 05/17/2018] [Accepted: 06/20/2018] [Indexed: 02/05/2023]
Abstract
BACKGROUND Dolutegravir (DTG) is a next-generation HIV integrase inhibitor (INI) with an increased genetic barrier to resistance with respect to raltegravir (RAL) or elvitegravir (EVG). Few data are available on the durability of DTG-containing regimens. OBJECTIVES We aimed at investigating the duration of the DTG-containing regimen, the occurrence of an HIV-1 RNA blip, and factors associated with DTG virological response. STUDY DESIGN From the Antiviral Response Cohort Analysis database, we selected 89 HIV-1-positive four-class-experienced subjects who started DTG after receiving RAL or EVG. Factors associated with durability and virological response were analysed by logistic regression. RESULTS After a median duration of 18.8 [0.4-76.2] months, 79/89 (88.8%) subjects were still on DTG. All subjects remaining on DTG at the end of follow-up had undetectable HIV-1 RNA, compared to 5/10 subjects who discontinued DTG. DTG discontinuation was less frequent in patients who had experienced ≥10 regimens (HR 0.11, p = 0.040). The probability of having an HIV-1 RNA positive value at the last follow-up significantly increased in patients with non-B HIV-1 subtype (HR 5.77, p < .001) and significantly decreased in patients with CD4 nadir >200/μL (HR 0.29, p = 0.038), with more than 10 previous regimens (HR 0.27, p = 0.040), and who harbored virus with IN mutations (HR 0.12, p = 0.023) at DTG start. CONCLUSIONS After previous exposure to first-generation INIs, treatment with DTG showed long durability and did not show virological rebound after virological suppression. Subjects infected with a non-B HIV-1 subtype had a greater risk of having detectable HIV-1 RNA at the last observation.
Collapse
Affiliation(s)
- S Rusconi
- Divisione Malattie Infettive, DIBIC Luigi Sacco, Università degli Studi di Milano, Italy.
| | | | - P Tau
- Divisione Malattie Infettive, DIBIC Luigi Sacco, Università degli Studi di Milano, Italy
| | - V Borghi
- Clinica Malattie Infettive, Modena, Italy
| | | | - R Maserati
- Ambulatorio Clinica Malattie Infettive, Fondazione Policlinico San Matteo, Pavia, Italy
| | | | - L Monno
- Clinica Malattie Infettive, Bari, Italy
| | - G Punzi
- Laboratorio di Virologia, Bari, Italy
| | - P Meraviglia
- Prima divisione di Malattie Infettive, Ospedale Luigi Sacco, Milano, Italy
| | - S Paolucci
- Laboratorio di Virologia, Fondazione Policlinico San Matteo, Pavia, Italy
| | - A Di Biagio
- Clinica Malattie Infettive, Azienda Ospedaliera Universitaria San Martino, Genova, Italy
| | - B Bruzzone
- Laboratorio di Igiene, Azienda Ospedaliera Universitaria San Martino, Genova, Italy
| | - A Mancon
- Laboratorio Microbiologia Clinica - Virologia - Bioterrorismo, Ospedale Luigi Sacco, ASST FBF-Sacco, Milano, Italy
| | - V Micheli
- Laboratorio Microbiologia Clinica - Virologia - Bioterrorismo, Ospedale Luigi Sacco, ASST FBF-Sacco, Milano, Italy
| | - M Zazzi
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, Italy
| |
Collapse
|
43
|
Koullias Y, Sax PE, Fields NF, Walensky RP, Hyle EP. Should We Be Testing for Baseline Integrase Resistance in Patients Newly Diagnosed With Human Immunodeficiency Virus? Clin Infect Dis 2018; 65:1274-1281. [PMID: 28605418 DOI: 10.1093/cid/cix542] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/07/2017] [Indexed: 12/30/2022] Open
Abstract
Background Current guidelines recommend genotype resistance testing at diagnosis to guide initial selection of antiretroviral therapy (ART). Many standard resistance genotypes exclude testing for resistance to integrase inhibitors ("IR testing"), although this class of drugs is a component of most recommended first-line regimens. Methods We compared the 96-week clinical outcomes and cost-effectiveness of 2 strategies: no IR testing vs IR testing performed at human immunodeficiency virus (HIV) diagnosis. The base case prevalence of transmitted integrase strand transfer inhibitor (INSTI)-resistant (INSTI-R) virus is estimated at 0.1%. With no IR testing, all patients start dolutegravir (DTG)-based ART after genotype; 12-week suppression rates are 90% (INSTI-susceptible [INSTI-S] virus) and 35% (INSTI-R virus). Those not suppressed at 12 weeks undergo IR testing; if diagnosed with INSTI-R virus, they change to ritonavir-boosted darunavir (DRV/r)-based ART. With IR testing, all patients are diagnosed with INSTI-S/INSTI-R virus prior to ART initiation and start DTG- or DRV/r-based regimens, respectively. Costs include IR tests (175 US dollars [USD]) and ART (41100-44900 USD/year). We examined the impact of key parameters in sensitivity analyses. Results IR testing resulted in worse clinical outcomes compared to no IR testing and increased costs by 200 USD/person/year. Prevalence of transmitted INSTI-R virus did not affect the favored strategy. No IR testing remained clinically preferred unless DTG suppression of INSTI-R virus was <20% or 96-week DRV/r suppression was >92%. If quality of life was worse with DRV/r- than DTG-based ART, no IR testing was clinically preferred over an even broader range of parameters. Conclusions In patients with newly diagnosed HIV, IR testing is projected to result in worse outcomes and is not cost-effective. Pretreatment assessment for INSTI resistance should not be recommended in treatment guidelines.
Collapse
Affiliation(s)
- Yiannis Koullias
- Department of Medicine, Brigham and Women's Hospital, Boston, MA.,Harvard Medical School, Boston, Massachusetts
| | - Paul E Sax
- Harvard Medical School, Boston, Massachusetts.,Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA
| | - Naomi F Fields
- Medical Practice Evaluation Center, Department of Medicine, Massachusetts General Hospital, Boston
| | - Rochelle P Walensky
- Harvard Medical School, Boston, Massachusetts.,Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA,Medical Practice Evaluation Center, Department of Medicine, Massachusetts General Hospital, Boston.,Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA
| | - Emily P Hyle
- Harvard Medical School, Boston, Massachusetts.,Medical Practice Evaluation Center, Department of Medicine, Massachusetts General Hospital, Boston.,Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA
| |
Collapse
|
44
|
HIV-1 integrase strand-transfer inhibitor resistance in southern Taiwan. Oncotarget 2018; 9:24927-24935. [PMID: 29861843 PMCID: PMC5982757 DOI: 10.18632/oncotarget.24837] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 03/11/2018] [Indexed: 01/04/2023] Open
Abstract
The use of antiretroviral therapy has reduced rates of mortality and morbidity in patients with human immunodeficiency virus/acquired immune deficiency syndrome(HIV/AIDS). However, transmission of drug-resistant strains poses a challenge to control the spread of HIV-1. Primary resistance to integrase strand-transfer inhibitors (INSTIs) is rare despite their increased use. The prevalence of transmitted drug resistance (TDR) to INSTIs was 0.9% in northern Taiwan. This study was to analyse the prevalence and risk factors of TDR to INSTIs in southern Taiwan. In this study, we enrolled antiretroviral treatment-naïve HIV-1-infected subjects who underwent voluntary counselling and testing from 2013 to 2016 in southern Taiwan. Genotypic drug resistance, coreceptor tropism (CRT) and INSTI resistance were determined. Logistic regression was used to analyse the risk factors for INSTI polymorphic substitution. Sequences were obtained from 184 consecutive individuals, of whom 96.7% were men who have sex with men and 3.3% were heterosexual. Of the patients, 10% (19/183) had hepatitis B and 33.3% (61/183) had syphilis infection. Subtype B HIV-1 strains were found in 96.1% of the patients. Fifteen patients (8.4%, 15/178) harboured nucleoside reverse transcriptase inhibitors, non-nucleoside reverse transcriptase inhibitors or protease inhibitors resistance. CCR-5 coreceptors were used by 71.4% (130/184) of the patients. None of the patients had INSTI resistance-associated mutations, however 16 patients had INSTI polymorphic substitutions, and they were associated with a higher HIV viral load (p = 0.03, OR 2.4, CI 1.1–5.3) and syphilis infection (p = 0.03, OR 3.7, CI 1.1–12.0). In conclusion, no signature INSTI resistance-associated mutations were detected in our cohort. Continued monitoring of TDR to INSTI is needed due to the increased use of INSTIs.
Collapse
|
45
|
Brado D, Obasa AE, Ikomey GM, Cloete R, Singh K, Engelbrecht S, Neogi U, Jacobs GB. Analyses of HIV-1 integrase sequences prior to South African national HIV-treatment program and available of integrase inhibitors in Cape Town, South Africa. Sci Rep 2018; 8:4709. [PMID: 29549274 PMCID: PMC5856838 DOI: 10.1038/s41598-018-22914-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/01/2018] [Indexed: 01/16/2023] Open
Abstract
HIV-Integrase (IN) has proven to be a viable target for highly specific HIV-1 therapy. We aimed to characterize the HIV-1 IN gene in a South African context and identify resistance-associated mutations (RAMs) against available first and second generation Integrase strand-transfer inhibitors (InSTIs). We performed genetic analyses on 91 treatment-naïve HIV-1 infected patients, as well as 314 treatment-naive South African HIV-1 IN-sequences, downloaded from Los Alamos HIV Sequence Database. Genotypic analyses revealed the absence of major RAMs in the cohort collected before the broad availability of combination antiretroviral therapy (cART) and INSTI in South Africa, however, occurred at a rate of 2.85% (9/314) in database derived sequences. RAMs were present at IN-positions 66, 92, 143, 147 and 148, all of which may confer resistance to Raltegravir (RAL) and Elvitegravir (EVG), but are unlikely to affect second-generation Dolutegravir (DTG), except mutations in the Q148 pathway. Furthermore, protein modeling showed, naturally occurring polymorphisms impact the stability of the intasome-complex and therefore may contribute to an overall potency against InSTIs. Our data suggest the prevalence of InSTI RAMs, against InSTIs, is low in South Africa, but natural polymorphisms and subtype-specific differences may influence the effect of individual treatment regimens.
Collapse
Affiliation(s)
- Dominik Brado
- Division of Virology, Institute for Virology and Immunobiology, Faculty of Medicine, University of Wuerzburg, 97080, Wuerzburg, Germany
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Adetayo Emmanuel Obasa
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa.
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, University of Stockholm, Stockholm, Sweden.
| | - George Mondinde Ikomey
- CSCCD, Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Yaoundé, Cameroon
| | - Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Western Cape, South Africa
| | - Kamalendra Singh
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, University of Stockholm, Stockholm, Sweden
- Department of Molecular Microbiology and Immunology, Columbia, MO, 65211, USA
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Susan Engelbrecht
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, University of Stockholm, Stockholm, Sweden
| | - Graeme Brendon Jacobs
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| |
Collapse
|
46
|
Ex-vivo antiretroviral potency of newer integrase strand transfer inhibitors cabotegravir and bictegravir in HIV type 1 non-B subtypes. AIDS 2018; 32:469-476. [PMID: 29239896 DOI: 10.1097/qad.0000000000001726] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To determine the antiretroviral activity of the integrase strand transfer inhibitors (INSTIs), raltegravir (RAL), elvitegravir (EVG), dolutegravir (DTG), cabotegravir (CAB) and bictegravir (BIC), against different subtypes as well as primary and acquired drug resistance mutations (DRMs) in a patient-cohort infected with diverse subtypes. DESIGN Biochemical and virological drug sensitivity analyses using patient-derived HIV type 1 (HIV-1) genes and cross-sectional/longitudinal clinical study. METHODS Assays for 50% inhibition of 3'-end processing (IC50-3EP), strand transfer (IC50-ST) and drug sensitivity for five INSTIs were done using patient-derived integrase or gag-pol genes from subtypes A1, B, C, 01_AE and 02_AG. Integrase from INSTI-naive (n = 270) and experienced (n = 96) patients were sequenced. RESULTS RAL had higher IC50-ST than the other INSTIs for all subtypes. EVG had higher IC50-ST for HIV 1 subtype C (P < 0.05) and 02_AG (P < 0.05) than HIV 1 subtype B (HIV-1B). DTG showed lower IC50-ST in HIV 1 subtype C than HIV-1B (P = 0.003). In CAB , the non-B subtypes showed lower IC50-ST (P < 0.05) than HIV-1B. In BIC, lower IC50-ST in 01_AE (P = 0.017) and 02_AG (P = 0.045) than HIV-1B. In drug sensitivity assay, inhibiting virus replication by 50% for DTG [median (IQR) 2.14 (1.3-2.56)], CAB [1.68 (1.34-2.55)] and BIC [1.07 (0.22-2.53)] were lower than RAL and EVG. One patient had a primary DRMs (0.3%, 1/270), but 17 (6.3%) had one major accessory DRM, of which 12 were E157Q. CONCLUSION The equal or higher potency in non-B subtypes of DTG, CAB and BIC compared with RAL and EVG confirms their suitability for use in countries dominated by non-B subtypes. Any impact of the high prevalence of major accessory mutations, especially E157Q, requires long-term follow-up studies.
Collapse
|
47
|
Nasir IA, Emeribe AU, Ojeamiren I, Aderinsayo Adekola H. Human Immunodeficiency Virus Resistance Testing Technologies and Their Applicability in Resource-Limited Settings of Africa. Infect Dis (Lond) 2017; 10:1178633717749597. [PMID: 29308013 PMCID: PMC5751912 DOI: 10.1177/1178633717749597] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 11/26/2017] [Indexed: 01/03/2023] Open
Abstract
There has been tremendous breakthrough in the development of technologies and protocols for counselling, testing, and surveillance of resistant human immunodeficiency virus strains for efficient prognosis and clinical management aimed at improving the quality of life of infected persons. However, we have not arrived at a point where services rendered using these technologies can be made affordable and accessible to resource-limited settings. There are several technologies for monitoring antiretroviral resistance, each with unique merits and demerits. In this study, we review the strengths and limitations of prospective and affordable technologies with emphasis on those that could be used in resource-limited settings.
Collapse
Affiliation(s)
- Idris Abdullahi Nasir
- Department of Medical Microbiology and Parasitology, College of Health Sciences, University of Ilorin, Ilorin, Nigeria.,Department of Medical Laboratory Services, University of Abuja Teaching Hospital, FCT Abuja, Nigeria.,Department of Medical Laboratory Science, College of Medical Sciences, University of Maiduguri, Maiduguri, Nigeria
| | | | - Iduda Ojeamiren
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Hafeez Aderinsayo Adekola
- Department of Medical Microbiology and Parasitology, College of Health Sciences, University of Ilorin, Ilorin, Nigeria
| |
Collapse
|
48
|
Fabrizio C, Lepore L, Lagioia A, Punzi G, Saracino A, Angarano G, Monno L. Comment on: Integrase strand-transfer inhibitor polymorphic and accessory resistance substitutions in patients with acute/recent HIV infection. J Antimicrob Chemother 2017; 72:1546-1547. [PMID: 28158344 DOI: 10.1093/jac/dkx014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
|
49
|
Drug resistance in B and non-B subtypes amongst subjects recently diagnosed as primary/recent or chronic HIV-infected over the period 2013-2016: Impact on susceptibility to first-line strategies including integrase strand-transfer inhibitors. J Glob Antimicrob Resist 2017; 10:106-112. [PMID: 28732792 DOI: 10.1016/j.jgar.2017.05.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/30/2017] [Accepted: 05/03/2017] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVES To characterize the prevalence of transmitted drug resistance mutations (TDRMs) by plasma analysis of 750 patients at the time of HIV diagnosis from January 1, 2013 to November 16, 2016 in the Veneto region (Italy), where all drugs included in the recommended first line therapies were prescribed, included integrase strand transfer inhibitors (InNSTI). METHODS TDRMs were defined according to the Stanford HIV database algorithm. RESULTS Subtype B was the most prevalent HIV clade (67.3%). A total of 92 patients (12.3%) were expected to be resistant to one drug at least, most with a single class mutation (60/68-88.2% in subtype B infected subjectsand 23/24-95.8% in non-B subjects) and affecting mainly NNRTIs. No significant differences were observed between the prevalence rates of TDRMs involving one or more drugs, except for the presence of E138A quite only in patients with B subtype and other NNRTI in subjects with non-B infection. The diagnosis of primary/recent infection was made in 73 patients (9.7%): they had almost only TDRMs involving a single class. Resistance to InSTI was studied in 484 subjects (53 with primary-recent infection), one patient had 143C in 2016, a total of thirteen 157Q mutations were detected (only one in primary/recent infection). CONCLUSIONS Only one major InSTI-TDRM was identified but monitoring of TDRMs should continue in the light of continuing presence of NNRTI-related mutation amongst newly diagnosed subjects, sometime impacting also to modern NNRTI drugs recommended in first-line therapy.
Collapse
|
50
|
Bradley-Stewart A, Urcia C, MacLean A, Aitken C, Gunson R. HIV-1 integrase inhibitor resistance among treatment naïve patients in the West of Scotland. J Clin Virol 2017; 92:7-10. [PMID: 28494325 DOI: 10.1016/j.jcv.2017.04.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 03/14/2017] [Accepted: 04/16/2017] [Indexed: 02/04/2023]
Abstract
BACKGROUND Transmitted integrase inhibitor resistance is rare, with only a small number of cases reported world-wide to date. OBJECTIVES The aim of this study was to assess whether transmitted integrase inhibitor resistance has occurred in Scotland and if so, could there be a case for performing genotypic integrase resistance testing at baseline. STUDY DESIGN The study population consisted of 106 treatment naïve, newly diagnosed, HIV positive patients. The patient samples were collected between October 2015 and March 2016 at the time of HIV diagnosis and prior to initiation of anti-retroviral therapy. The integrase region was amplified and sequenced. RESULTS We detected integrase inhibitor resistance (T66I/T) at baseline in one patient sample. This is a non-polymorphic mutation seen in patients receiving elvitegravir which confers high-level resistance to elvitegravir and intermediate resistance to raltegravir. A further 10 patients had accessory mutations which have minimal or no effect on susceptibility to integrase inhibitors. CONCLUSIONS Transmitted integrase inhibitor resistance remains rare. The results of the present study do not support performing integrase resistance testing at baseline.
Collapse
Affiliation(s)
- A Bradley-Stewart
- West of Scotland Specialist Virology Centre, Level 5, New Lister Building, 10-16 Alexandra Parade, Glasgow G31 2ER, United Kingdom.
| | - C Urcia
- West of Scotland Specialist Virology Centre, Level 5, New Lister Building, 10-16 Alexandra Parade, Glasgow G31 2ER, United Kingdom
| | - A MacLean
- West of Scotland Specialist Virology Centre, Level 5, New Lister Building, 10-16 Alexandra Parade, Glasgow G31 2ER, United Kingdom
| | - C Aitken
- West of Scotland Specialist Virology Centre, Level 5, New Lister Building, 10-16 Alexandra Parade, Glasgow G31 2ER, United Kingdom
| | - R Gunson
- West of Scotland Specialist Virology Centre, Level 5, New Lister Building, 10-16 Alexandra Parade, Glasgow G31 2ER, United Kingdom
| |
Collapse
|