1
|
Mokgethi PT, Choga WT, Maruapula D, Moraka NO, Seatla KK, Bareng OT, Ditshwanelo DD, Mulenga G, Mohammed T, Kaumba PM, Chihungwa M, Marukutira T, Moyo S, Koofhethile CK, Dickinson D, Mpoloka SW, Gaseitsiwe S. High prevalence of pre-treatment and acquired HIV-1 drug resistance mutations among non-citizens living with HIV in Botswana. Front Microbiol 2024; 15:1338191. [PMID: 38476948 PMCID: PMC10929613 DOI: 10.3389/fmicb.2024.1338191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/08/2024] [Indexed: 03/14/2024] Open
Abstract
Background Approximately 30,000 non-citizens are living with HIV in Botswana, all of whom as of 2020 are eligible to receive free antiretroviral treatment (ART) within the country. We assessed the prevalence of HIV-1 mutational profiles [pre-treatment drug resistance (PDR) and acquired drug resistance (ADR)] among treatment-experienced (TE) and treatment-naïve (TN) non-citizens living with HIV in Botswana. Methods A total of 152 non-citizens living with HIV were enrolled from a migrant HIV clinic at Independence Surgery, a private practice in Botswana from 2019-2021. Viral RNA isolated from plasma samples were genotyped for HIV drug resistance (HIVDR) using Sanger sequencing. Major known HIV drug resistance mutations (DRMs) in the pol region were determined using the Stanford HIV Drug Resistance Database. The proportions of HIV DRMs amongst TE and TN non-citizens were estimated with 95% confidence intervals (95% CI) and compared between the two groups. Results A total of 60/152 (39.5%) participants had a detectable viral load (VL) >40 copies/mL and these were included in the subsequent analyses. The median age at enrollment was 43 years (Q1, Q3: 38-48). Among individuals with VL > 40 copies/mL, 60% (36/60) were treatment-experienced with 53% (19/36) of them on Atripla. Genotyping had a 62% (37/60) success rate - 24 were TE, and 13 were TN. A total of 29 participants (78.4, 95% CI: 0.12-0.35) had major HIV DRMs, including at least one non-nucleoside reverse transcriptase inhibitor (NNRTI) associated DRM. In TE individuals, ADR to any antiretroviral drug was 83.3% (20/24), while for PDR was 69.2% (9/13). The most frequent DRMs were nucleoside reverse transcriptase inhibitors (NRTIs) M184V (62.1%, 18/29), NNRTIs V106M (41.4%, 12/29), and K103N (34.4%, 10/29). No integrase strand transfer inhibitor-associated DRMs were reported. Conclusion We report high rates of PDR and ADR in ART-experienced and ART-naïve non-citizens, respectively, in Botswana. Given the uncertainty of time of HIV acquisition and treatment adherence levels in this population, routine HIV-1C VL monitoring coupled with HIVDR genotyping is crucial for long-term ART success.
Collapse
Affiliation(s)
- Patrick T. Mokgethi
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Wonderful T. Choga
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Center of Epidemic Response and Innovation, Faculty of Data Sciences, Stellenbosch University, Cape Town, South Africa
- School of Allied Health Professionals, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | | | - Natasha O. Moraka
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- School of Allied Health Professionals, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Kaelo K. Seatla
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Ontlametse T. Bareng
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- School of Allied Health Professionals, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | | | | | | | - Pearl M. Kaumba
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | | | - Tafireyi Marukutira
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Public Health, Burnet Institute, Melbourne, VIC, Australia
- Department of Epidemiology, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Catherine K. Koofhethile
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | | | | | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| |
Collapse
|
2
|
Richard K, Andrae-Marobela K, Tietjen I. An ethnopharmacological survey of medicinal plants traditionally used by the BaKalanga people of the Tutume subdistrict in Central Botswana to manage HIV/AIDS, HIV-associated conditions, and other health conditions. JOURNAL OF ETHNOPHARMACOLOGY 2023:116759. [PMID: 37301306 DOI: 10.1016/j.jep.2023.116759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/21/2023] [Accepted: 06/07/2023] [Indexed: 06/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE While access to antiretroviral therapy (ART) continues to improve worldwide, HIV infection and AIDS persist as serious health challenges, particularly in sub-Saharan Africa. Complementary and Alternative Medicines (CAM), as part of indigenous and pluralistic medical systems, are important contributors to primary health care worldwide. However, this knowledge remains relatively undocumented in many parts of sub-Saharan Africa such as the Tutume subdistrict of Central Botswana, where CAM is widely used including potentially for HIV/AIDS and HIV-associated conditions. AIM OF THE STUDY To explore the extent to which CAM is used by the BaKalanga Peoples of the Tutume subdistrict, we performed an exploratory community-based project to record medicinal plant use from this relatively undocumented region, with a particular focus on species used for management of HIV/AIDS and HIV-associated conditions. MATERIALS AND METHODS Using the snowball sampling technique, we recruited 13 Traditional Health Practitioners (THPs) and conducted in-depth interviews to explore medicinal plant uses and treatment regimens. Plant specimens were collected and bio-authenticated. RESULTS We documented 83 plant species used as CAM to treat or manage a variety of conditions including HIV/AIDS, HIV-associated conditions, and other health conditions. Plants from the family Leguminosae were most frequently reported, comprising 21 species (25.3%), followed by 5 from both Euphorbiaceae and Combretaceae families (6.0%). Four plants (4.8%) were used specifically to manage HIV (Lannea edulis (Sond.) Engl. root, Aloe zebrina Baker root, Myrothamnus flabellifolia Welw. whole plant, and Harpagophytum procumbens var. subulobatum (Engl.) tuber), while an additional 7 (8.4%) were reported specifically for treating combinations of HIV-related symptoms. Notably, 25 (30.1%) have not been reported previously as CAM and/or lack reported bioactivity data. CONCLUSIONS To our knowledge, this is the first detailed ethnobotanical survey of CAM used by the BaKalanga Peoples of the Tutume subdistrict to manage HIV/AIDS and HIV-associated and other health conditions.
Collapse
Affiliation(s)
- Khumoekae Richard
- Faculty of Health Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada; The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA.
| | - Kerstin Andrae-Marobela
- Department of Biological Sciences, University of Botswana, Block 235/217, Gaborone, Botswana; Center for Scientific Research, Indigenous Knowledge & Innovation (CesrIKi), PO Box 70237, Gaborone, Botswana.
| | - Ian Tietjen
- Faculty of Health Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada; The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA.
| |
Collapse
|
3
|
Mokaleng B, Choga WT, Bareng OT, Maruapula D, Ditshwanelo D, Kelentse N, Mokgethi P, Moraka NO, Motswaledi MS, Tawe L, Koofhethile CK, Moyo S, Zachariah M, Gaseitsiwe S. No Difference in the Prevalence of HIV-1 gag Cytotoxic T-Lymphocyte-Associated Escape Mutations in Viral Sequences from Early and Late Parts of the HIV-1 Subtype C Pandemic in Botswana. Vaccines (Basel) 2023; 11:1000. [PMID: 37243104 PMCID: PMC10221913 DOI: 10.3390/vaccines11051000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
HIV is known to accumulate escape mutations in the gag gene in response to the immune response from cytotoxic T lymphocytes (CTLs). These mutations can occur within an individual as well as at a population level. The population of Botswana exhibits a high prevalence of HLA*B57 and HLA*B58, which are associated with effective immune control of HIV. In this retrospective cross-sectional investigation, HIV-1 gag gene sequences were analyzed from recently infected participants across two time periods which were 10 years apart: the early time point (ETP) and late time point (LTP). The prevalence of CTL escape mutations was relatively similar between the two time points-ETP (10.6%) and LTP (9.7%). The P17 protein had the most mutations (9.4%) out of the 36 mutations that were identified. Three mutations (A83T, K18R, Y79H) in P17 and T190A in P24 were unique to the ETP sequences at a prevalence of 2.4%, 4.9%, 7.3%, and 5%, respectively. Mutations unique to the LTP sequences were all in the P24 protein, including T190V (3%), E177D (6%), R264K (3%), G248D (1%), and M228L (11%). Mutation K331R was statistically higher in the ETP (10%) compared to the LTP (1%) sequences (p < 0.01), while H219Q was higher in the LTP (21%) compared to the ETP (5%) (p < 0.01). Phylogenetically, the gag sequences clustered dependently on the time points. We observed a slower adaptation of HIV-1C to CTL immune pressure at a population level in Botswana. These insights into the genetic diversity and sequence clustering of HIV-1C can aid in the design of future vaccine strategies.
Collapse
Affiliation(s)
- Baitshepi Mokaleng
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone 999106, Botswana; (M.S.M.); (L.T.); (M.Z.)
| | - Wonderful Tatenda Choga
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone 999106, Botswana; (M.S.M.); (L.T.); (M.Z.)
| | - Ontlametse Thato Bareng
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone 999106, Botswana; (M.S.M.); (L.T.); (M.Z.)
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
| | - Doreen Ditshwanelo
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
| | - Nametso Kelentse
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
| | - Patrick Mokgethi
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
- Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone 999106, Botswana
| | - Natasha Onalenna Moraka
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone 999106, Botswana; (M.S.M.); (L.T.); (M.Z.)
| | - Modisa Sekhamo Motswaledi
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone 999106, Botswana; (M.S.M.); (L.T.); (M.Z.)
| | - Leabaneng Tawe
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone 999106, Botswana; (M.S.M.); (L.T.); (M.Z.)
| | - Catherine Kegakilwe Koofhethile
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Matshediso Zachariah
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone 999106, Botswana; (M.S.M.); (L.T.); (M.Z.)
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| |
Collapse
|
4
|
Bareng OT, Choga WT, Maphorisa ST, Seselamarumo S, Seatla KK, Mokgethi PT, Maruapula D, Mogwele ML, Ditshwanelo D, Moraka NO, Gobe I, Motswaledi MS, Makhema JM, Musonda R, Shapiro R, Essex M, Novitsky V, Moyo S, Gaseitsiwe S. HIV-1C in-House RNA-Based Genotyping Assay for Detection of Drug Resistance Mutations in Samples with Low-Level Viral Loads. Infect Drug Resist 2022; 15:7565-7576. [PMID: 36582452 PMCID: PMC9792565 DOI: 10.2147/idr.s388816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/08/2022] [Indexed: 12/24/2022] Open
Abstract
Purpose Monitoring HIV-1 drug resistance mutations (DRM) in treated patients on combination antiretroviral therapy (cART) with a detectable HIV-1 viral load (VL) is important for the selection of appropriate cART. Currently, there is limited data on HIV DRM at low-level viremia (LLV) (VL 401-999 copies/mL) due to the use of a threshold of VL ≥1000 copies/mL for HIV DRM testing. We here assess the performance of an in-house HIV drug resistance genotyping assay using plasma for the detection of DRM at LLV. Methods We used a total of 96 HIV plasma samples from the population-based Botswana Combination Prevention Project (BCPP). The samples were stratified by VL groups: 50 samples had LLV, defined as 401-999 copies/mL, and 46 had ≥1000 copies/mL. HIV pol (PR and RT) region was amplified and sequenced using an in-house genotyping assay with BigDye sequencing chemistry. Known HIV DRMs were identified using the Stanford HIV Drug Resistance Database. Genotyping success rate between the two groups was estimated and compared using the comparison of proportions test. Results The overall genotyping success rate was 79% (76/96). For VL groups, the genotyping success was 72% (36/50) at LLV and 87% (40/46) at VL ≥1000 copies/mL. Among generated sequences, the overall prevalence of individuals with at least 1 major or intermediate-associated DRM was 24% (18/76). The proportions of NNRTI-, NRTI- and PI-associated resistance mutations were 28%, 24%, and 0%, respectively. The most predominant mutations detected were K103N (18%) and M184V (12%) in NNRTI- and NRTI-associated mutations, respectively. The prevalence of DRM was 17% (6/36) at LLV and 30% (12/40) at VL ≥1000 copies/mL. Conclusion The in-house HIV genotyping assay successfully genotyped 72% of LLV samples and was able to detect 17% of DRM amongst them. Our results highlight the possibility and clinical significance of genotyping HIV among individuals with LLV.
Collapse
Affiliation(s)
- Ontlametse T Bareng
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Wonderful T Choga
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | | | | | - Kaelo K Seatla
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Patrick T Mokgethi
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | | | - Doreen Ditshwanelo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,Department of Biological Science and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
| | | | - Irene Gobe
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Modisa S Motswaledi
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Joseph M Makhema
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Max Essex
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Vlad Novitsky
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Correspondence: Simani Gaseitsiwe, Botswana Harvard AIDS Institute Partnership, Private Bag BO320, Bontleng, Gaborone, Botswana, Tel +267 390 2671, Fax +267 390 1284, Email
| |
Collapse
|
5
|
Bareng OT, Seselamarumo S, Seatla KK, Choga WT, Bakae B, Maruapula D, Kelentse N, Moraka NO, Mokaleng B, Mokgethi PT, Ditlhako TR, Pretorius-Holme M, Mbulawa MB, Lebelonyane R, Bile EC, Gaolathe T, Shapiro R, Makhema JM, Lockman S, Essex M, Novitsky V, Mpoloka SW, Moyo S, Gaseitsiwe S. Doravirine-associated resistance mutations in antiretroviral therapy naïve and experienced adults with HIV-1 subtype C infection in Botswana. J Glob Antimicrob Resist 2022; 31:128-134. [PMID: 35973671 PMCID: PMC9750894 DOI: 10.1016/j.jgar.2022.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/25/2022] [Accepted: 08/09/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES There are limited data on the prevalence of doravirine (DOR)-associated drug resistance mutations in people with HIV (PWH) in Botswana. This cross-sectional, retrospective study aimed to explore the prevalence of DOR-associated resistance mutations among ART-naïve and -experienced PWH in Botswana enrolled in the population-based Botswana Combination Prevention Project (BCPP). METHODS A total of 6078 HIV-1C pol sequences were analysed for DOR-associated resistance mutations using the Stanford HIV drug resistance database, and their levels were predicted according to the Stanford DRM penalty scores and resistance interpretation. Virologic failure was defined as HIV-1 RNA load (VL) >400 copies/mL. RESULTS Among 6078 PWH, 5999 (99%) had known ART status, and 4529/5999 (79%) were on ART at time of sampling. The suppression rate among ART-experienced was 4517/4729 (96%). The overall prevalence of any DOR-associated resistance mutations was 181/1473 (12.3% [95% confidence interval {CI}: 10.7-14.1]); by ART status: 42/212 (19.8% [95% CI: 14.7-25.4]) among ART-failing individuals (VL ≥400 copies/mL) and 139/1261 (11.0% [95% CI: 9.3-12.9]) among ART-naïve individuals (P < 0.01). Intermediate DOR-associated resistance mutations were observed in 106/1261 (7.8% [95% CI: 6.9-10.1]) in ART-naïve individuals and 29/212 (13.7% [95% CI: 9.4-8.5]) among ART-experienced participants (P < 0.01). High-level DOR-associated resistance mutations were observed in 33/1261 (2.6% [95% CI: 1.8-3.7]) among ART-naïve and 13/212 (6.1% [95% CI: 3.6-10.8]) among ART-failing PWH (P < 0.01). PWH failing ART with at least one EFV/NVP-associated resistance mutation had high prevalence 13/67 (19.4%) of high-level DOR-associated resistance mutations. CONCLUSION DOR-associated mutations were rare (11.0%) among ART-naive PWH but present in 62.7% of Botswana individuals who failed NNRTI-based ART with at least one EFV/NVP-associated resistance mutation. Testing for HIV drug resistance should underpin the use of DOR in PWH who have taken first-generation NNRTIs.
Collapse
Affiliation(s)
- Ontlametse T Bareng
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Medical Sciences, Faculty of Allied Health Professions, University of Botswana, Gaborone, Botswana
| | - Sekgabo Seselamarumo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | - Kaelo K Seatla
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Medical Sciences, Faculty of Allied Health Professions, University of Botswana, Gaborone, Botswana
| | - Wonderful T Choga
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Blessing Bakae
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | - Nametso Kelentse
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Medical Sciences, Faculty of Allied Health Professions, University of Botswana, Gaborone, Botswana
| | - Natasha O Moraka
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Division of Medical Virology, Stellenbosch University, Cape Town, South Africa
| | - Baitshepi Mokaleng
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Medical Sciences, Faculty of Allied Health Professions, University of Botswana, Gaborone, Botswana
| | - Patrick T Mokgethi
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | | | - Molly Pretorius-Holme
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | | | - Ebi Celestin Bile
- FHI 360, Department of Clinical Sciences, Durham, North Carolina, USA
| | | | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Joseph M Makhema
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Shahin Lockman
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA; Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Max Essex
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Vlad Novitsky
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Sununguko W Mpoloka
- Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
| |
Collapse
|
6
|
Maruapula D, Seatla KK, Morerinyane O, Molebatsi K, Giandhari J, de Oliveira T, Musonda RM, Leteane M, Mpoloka SW, Rowley CF, Moyo S, Gaseitsiwe S. Low-frequency HIV-1 drug resistance mutations in antiretroviral naïve individuals in Botswana. Medicine (Baltimore) 2022; 101:e29577. [PMID: 35838991 PMCID: PMC11132386 DOI: 10.1097/md.0000000000029577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/27/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Individuals living with human immunodeficiency virus (HIV) who experience virological failure (VF) after combination antiretroviral therapy (cART) initiation may have had low-frequency drug resistance mutations (DRMs) at cART initiation. There are no data on low-frequency DRMs among cART-naïve HIV-positive individuals in Botswana. METHODS We evaluated the prevalence of low-frequency DRMs among cART-naïve individuals previously sequenced using Sanger sequencing. The generated pol amplicons were sequenced by next-generation sequencing. RESULTS We observed low-frequency DRMs (detected at <20% in 33/103 (32%) of the successfully sequenced individuals, of whom four also had mutations detected at >20%. K65R was the most common low-frequency DRM detected in 8 individuals. Eighty-two of the 103 individuals had follow-up viral load data while on cART. Twenty-seven of the 82 individuals harbored low-frequency DRMs. Only 12 of 82 individuals experienced VF. The following low-frequency DRMs were observed in four individuals experiencing VF: K65R, K103N, V108I, and Y188C. No statistically significant difference was observed in the prevalence of low-frequency DRMs between individuals experiencing VF (4/12) and those not experiencing VF (23/70) (P = .97). However, individuals with non-nucleoside reverse transcriptase inhibitors-associated low-frequency DRMs were 2.68 times more likely to experience VF (odds ratio, 2.68; 95% confidential interval, 0.4-13.9) compared with those without (P = .22). CONCLUSION Next-generation sequencing was able to detect low-frequency DRMs in this cohort in Botswana, but these DRMs did not contribute significantly to VF.
Collapse
Affiliation(s)
- Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Kaelo K. Seatla
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- School of Allied Health Professions, University of Botswana, Gaborone, Botswana
| | | | - Kesaobaka Molebatsi
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Statistics, University of Botswana, Gaborone, Botswana
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Rosemary M. Musonda
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Melvin Leteane
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Sununguko W Mpoloka
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Christopher F. Rowley
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA
| |
Collapse
|
7
|
Maruapula D, MacLeod IJ, Moyo S, Musonda R, Seatla K, Molebatsi K, Leteane M, Essex M, Gaseitsiwe S, Rowley CF. Use of a mutation-specific genotyping method to assess for HIV-1 drug resistance in antiretroviral-naïve HIV-1 Subtype C-infected patients in Botswana. AAS Open Res 2021; 3:50. [PMID: 34036243 PMCID: PMC8112461 DOI: 10.12688/aasopenres.13107.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2021] [Indexed: 11/20/2022] Open
Abstract
Background: HIV-1 drug resistance poses a major threat to the success of antiretroviral therapy. The high costs of available HIV drug resistance assays prohibit their routine usage in resource-limited settings. Pan-degenerate amplification and adaptation (PANDAA), a focused genotyping approach based on quantitative PCR (qPCR), promises a fast and cost-effective way to detect HIV drug resistance mutations (HIVDRMs). Given the high cost of current genotyping methods, we sought to use PANDAA for screening key HIVDRMs in antiretroviral-naïve individuals at codons 103, 106 and 184 of the HIV-1 reverse transcriptase gene. Mutations selected at these positions have been shown to be the most common driver mutations in treatment failure. Methods: A total of 103 samples from antiretroviral-naïve individuals previously genotyped by Sanger population sequencing were used to assess and verify the performance of PANDAA. PANDAA samples were run on the ABI 7500 Sequence Detection System to genotype the K103N, V106M and M184V HIVDRMs. In addition, the cost per sample and reaction times were compared. Results: Sanger population sequencing and PANDAA detected K103N mutation in three (2.9%) out of 103 participants. There was no evidence of baseline V106M and M184V mutations observed in our study. To genotype the six HIVDRMs it costs approximately 40 USD using PANDAA, while the reagents cost per test for Sanger population sequencing is approximately 100 USD per sample. PANDAA was performed quicker compared to Sanger sequencing, 2 hours for PANDAA versus 15 hours for Sanger sequencing. Conclusion: The performance of PANDAA and Sanger population sequencing demonstrated complete concordance. PANDAA could improve patient management by providing quick and relatively cheap access to drug-resistance information.
Collapse
Affiliation(s)
- Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- University of Botswana, Gaborone, Botswana
| | - Iain J. MacLeod
- Harvard T.H Chan School of Public Health, Boston, MA, USA
- Aldatu Biosciences, Watertown, MA, USA
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard T.H Chan School of Public Health, Boston, MA, USA
| | | | - Kaelo Seatla
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- University of Botswana, Gaborone, Botswana
| | - Kesaobaka Molebatsi
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- University of Botswana, Gaborone, Botswana
| | | | - Max Essex
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard T.H Chan School of Public Health, Boston, MA, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard T.H Chan School of Public Health, Boston, MA, USA
| | - Christopher F. Rowley
- Harvard T.H Chan School of Public Health, Boston, MA, USA
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| |
Collapse
|
8
|
MacLeod IJ, Rowley CF, Essex M. PANDAA intentionally violates conventional qPCR design to enable durable, mismatch-agnostic detection of highly polymorphic pathogens. Commun Biol 2021; 4:227. [PMID: 33603155 PMCID: PMC7892852 DOI: 10.1038/s42003-021-01751-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023] Open
Abstract
Sensitive and reproducible diagnostics are fundamental to containing the spread of existing and emerging pathogens. Despite the reliance of clinical virology on qPCR, technical challenges persist that compromise their reliability for sustainable epidemic containment as sequence instability in probe-binding regions produces false-negative results. We systematically violated canonical qPCR design principles to develop a Pan-Degenerate Amplification and Adaptation (PANDAA), a point mutation assay that mitigates the impact of sequence variation on probe-based qPCR performance. Using HIV-1 as a model system, we optimized and validated PANDAA to detect HIV drug resistance mutations (DRMs). Ultra-degenerate primers with 3' termini overlapping the probe-binding site adapt the target through site-directed mutagenesis during qPCR to replace DRM-proximal sequence variation. PANDAA-quantified DRMs present at frequency ≥5% (2 h from nucleic acid to result) with a sensitivity and specificity of 96.9% and 97.5%, respectively. PANDAA is an innovative advancement with applicability to any pathogen where target-proximal genetic variability hinders diagnostic development.
Collapse
Affiliation(s)
- Iain J MacLeod
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA.
- Botswana-Harvard AIDS Institute Partnership, Private Bag, Gaborone, Botswana.
| | - Christopher F Rowley
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA
- Botswana-Harvard AIDS Institute Partnership, Private Bag, Gaborone, Botswana
- Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - M Essex
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA
- Botswana-Harvard AIDS Institute Partnership, Private Bag, Gaborone, Botswana
| |
Collapse
|
9
|
Moyo S, Hunt G, Zuma K, Zungu M, Marinda E, Mabaso M, Kana V, Kalimashe M, Ledwaba J, Naidoo I, Takatshana S, Matjokotja T, Dietrich C, Raizes E, Diallo K, Kindra G, Mugore L, Rehle T. HIV drug resistance profile in South Africa: Findings and implications from the 2017 national HIV household survey. PLoS One 2020; 15:e0241071. [PMID: 33147285 PMCID: PMC7641411 DOI: 10.1371/journal.pone.0241071] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND HIV drug resistance (HIVDR) testing was included in the 2017 South African national HIV household survey. We describe the prevalence of HIVDR by drug class, age, sex and antiretroviral drugs (ARV) status. METHODS Dried blood were spots tested for HIV, with Viral load (VL), exposure to ARVs and HIVDR testing among those HIV positive. HIVDR testing was conducted on samples with VL ≥1000 copies/ml using Next Generation Sequencing. Weighted percentages of HIVDR are reported. RESULTS 697/1,105 (63%) of HIV positive samples were sequenced. HIVDR was detected in samples from 200 respondents (27.4% (95% confidence interval (CI) 22.8-32.6)). Among these 130 (18.9% (95% CI 14.8-23.8)), had resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs) only, 63 (7.8% (95% CI 5.6-10.9)) resistance to NNRTIs and nucleoside reverse transcriptase inhibitors, and 3 (0.5% (95% CI 0.1-2.1)) resistance to protease inhibitors. Sixty-five (55.7% (95% CI 42.6-67.9) of ARV-positive samples had HIVDR compared to 112 (22.8% (95% CI 17.7-28.7)), in ARV-negative samples. HIVDR was found in 75.6% (95% CI 59.2-87.3), n = 27, samples from respondents who reported ARV use but tested ARV-negative, and in 15.3% (95% CI 6.3-32.8), n = 7, respondents who reported no ARV use and tested ARV-negative. There were no significant age and sex differences in HIVDR. CONCLUSION 27% of virally unsuppressed respondents had HIVDR, increasing to 75% among those who had discontinued ARV. Our findings support strengthening first-line ARV regimens by including drugs with a higher resistance barrier and treatment adherence strategies, and close monitoring of HIVDR.
Collapse
Affiliation(s)
- Sizulu Moyo
- Human Sciences Research Council, Pretoria, South Africa
- School of Public Health, University of Cape Town, Cape Town, South Africa
| | - Gillian Hunt
- Centre for HIV and STIs, National Institute of Communicable Diseases, Johannesburg, South Africa
| | | | - Mpumi Zungu
- Human Sciences Research Council, Pretoria, South Africa
| | - Edmore Marinda
- Human Sciences Research Council, Pretoria, South Africa
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Vibha Kana
- Centre for HIV and STIs, National Institute of Communicable Diseases, Johannesburg, South Africa
| | - Monalisa Kalimashe
- Centre for HIV and STIs, National Institute of Communicable Diseases, Johannesburg, South Africa
| | - Johanna Ledwaba
- Centre for HIV and STIs, National Institute of Communicable Diseases, Johannesburg, South Africa
| | | | | | | | - Cheryl Dietrich
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Elliot Raizes
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Karidia Diallo
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Gurpreet Kindra
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Linnetie Mugore
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Thomas Rehle
- School of Public Health, University of Cape Town, Cape Town, South Africa
| |
Collapse
|
10
|
Kelentse N, Moyo S, Mogwele M, Lechiile K, Moraka NO, Maruapula D, Seatla KK, Esele L, Molebatsi K, Leeme TB, Lawrence DS, Musonda R, Kasvosve I, Harrison TS, Jarvis JN, Gaseitsiwe S. Differences in human immunodeficiency virus-1C viral load and drug resistance mutation between plasma and cerebrospinal fluid in patients with human immunodeficiency virus-associated cryptococcal meningitis in Botswana. Medicine (Baltimore) 2020; 99:e22606. [PMID: 33031315 PMCID: PMC7544309 DOI: 10.1097/md.0000000000022606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 08/14/2020] [Accepted: 09/07/2020] [Indexed: 11/26/2022] Open
Abstract
To determine effects of cryptococcal meningitis (CM) on human immunodeficiency virus (HIV)-1C cerebrospinal fluid (CSF) viral escape, CSF/plasma viral discordance, and drug resistance mutation (DRM) discordance between CSF and plasma compartments, we compared CSF and plasma viral load (VL) and DRMs in individuals with HIV-associated CM in Botswana.This cross-sectional study utilized 45 paired CSF/plasma samples from participants in a CM treatment trial (2014-2016). HIV-1 VL was determined and HIV-1 protease and reverse transcriptase genotyping performed. DRMs were determined using the Stanford HIV database. CSF viral escape was defined as HIV-1 ribonucleic acid ≥0.5 log10 higher in CSF than plasma and VL discordance as CSF VL > plasma VL.HIV-1 VL was successfully measured in 39/45 pairs, with insufficient sample volume in 6; 34/39 (87.2%) participants had detectable HIV-1 in plasma and CSF, median 5.1 (interquartile range: 4.7-5.7) and 4.6 (interquartile range:3.7-4.9) log10 copies/mL, respectively (P≤.001). CSF viral escape was present in 1/34 (2.9%) and VL discordance in 6/34 (17.6%). Discordance was not associated with CD4 count, antiretroviral status, fungal burden, CSF lymphocyte percentage nor mental status. Twenty-six of 45 (57.8%) CSF/plasma pairs were successfully sequenced. HIV-1 DRM discordance was found in 3/26 (11.5%); 1 had I84IT and another had M46MI in CSF only. The third had K101E in plasma and V106 M in CSF.Our findings suggest that HIV-1 escape and DRM discordance may occur at lower rates in participants with advanced HIV-disease and CM compared to those with HIV associated neurocognitive impairment.
Collapse
Affiliation(s)
- Nametso Kelentse
- Botswana Harvard AIDS Institute Partnership
- University of Botswana, Department of Medical Laboratory Sciences, Gaborone, Botswana
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, United States
| | - Mompati Mogwele
- Botswana Harvard AIDS Institute Partnership
- University of Botswana, Department of Biological Sciences, Gaborone, Botswana
| | | | - Natasha O. Moraka
- Botswana Harvard AIDS Institute Partnership
- Stellenbosch University, Department of Pathology, Stellenbosch, South Africa
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership
- University of Botswana, Department of Biological Sciences, Gaborone, Botswana
| | - Kaelo K. Seatla
- Botswana Harvard AIDS Institute Partnership
- University of Botswana, Department of Medical Laboratory Sciences, Gaborone, Botswana
| | | | - Kesaobaka Molebatsi
- Botswana Harvard AIDS Institute Partnership
- University of Botswana, Department of Statistics, Gaborone, Botswana
| | - Tshepo B. Leeme
- Botswana Harvard AIDS Institute Partnership
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
| | - David S. Lawrence
- Botswana Harvard AIDS Institute Partnership
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Rosemary Musonda
- Botswana Harvard AIDS Institute Partnership
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, United States
| | - Ishmael Kasvosve
- University of Botswana, Department of Medical Laboratory Sciences, Gaborone, Botswana
| | - Thomas S. Harrison
- Centre for Global Health, Institute for Infection and Immunity, St. George's University of London, United Kingdom
| | - Joseph N. Jarvis
- Botswana Harvard AIDS Institute Partnership
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, The London School of Hygiene and Tropical Medicine, London, United Kingdom
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, United States
| |
Collapse
|
11
|
Maruapula D, MacLeod IJ, Moyo S, Musonda R, Seatla K, Molebatsi K, Leteane M, Essex M, Gaseitsiwe S, Rowley CF. Use of a mutation-specific genotyping method to assess for HIV-1 drug resistance in antiretroviral-naïve HIV-1 Subtype C-infected patients in Botswana. AAS Open Res 2020; 3:50. [PMID: 34036243 PMCID: PMC8112461 DOI: 10.12688/aasopenres.13107.1] [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] [Accepted: 07/29/2020] [Indexed: 10/20/2023] Open
Abstract
Background: HIV-1 drug resistance poses a major threat to the success of antiretroviral therapy. The high costs of available HIV drug resistance assays prohibit their routine usage in resource-limited settings. Pan-degenerate amplification and adaptation (PANDAA), a focused genotyping approach based on quantitative PCR (qPCR), promises a fast and cost-effective way to detect HIV drug resistance mutations (HIVDRMs). Given the high cost of current genotyping methods, we sought to use PANDAA for screening key HIVDRMs in antiretroviral-naïve individuals at codons 103, 106 and 184 of the HIV-1 reverse transcriptase gene. Mutations selected at these positions have been shown to be the most common driver mutations in treatment failure. Methods: A total of 103 samples from antiretroviral-naïve individuals previously genotyped by Sanger population sequencing were used to assess and verify the performance of PANDAA. PANDAA samples were run on the ABI 7500 Sequence Detection System to genotype the K103N, V106M and M184V HIVDRMs. In addition, the cost per sample and reaction times were compared. Results: Sanger population sequencing and PANDAA detected K103N mutation in three (2.9%) out of 103 participants. There was no evidence of baseline V106M and M184V mutations observed in our study. To genotype the six HIVDRMs it costs approximately 40 USD using PANDAA, while the reagents cost per test for Sanger population sequencing is approximately 100 USD per sample. PANDAA was performed quicker compared to Sanger sequencing, 2 hours for PANDAA versus 15 hours for Sanger sequencing. Conclusion: The performance of PANDAA and Sanger population sequencing demonstrated complete concordance. PANDAA could improve patient management by providing quick and relatively cheap access to drug-resistance information.
Collapse
Affiliation(s)
- Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- University of Botswana, Gaborone, Botswana
| | - Iain J. MacLeod
- Harvard T.H Chan School of Public Health, Boston, MA, USA
- Aldatu Biosciences, Watertown, MA, USA
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard T.H Chan School of Public Health, Boston, MA, USA
| | | | - Kaelo Seatla
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- University of Botswana, Gaborone, Botswana
| | - Kesaobaka Molebatsi
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- University of Botswana, Gaborone, Botswana
| | | | - Max Essex
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard T.H Chan School of Public Health, Boston, MA, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard T.H Chan School of Public Health, Boston, MA, USA
| | - Christopher F. Rowley
- Harvard T.H Chan School of Public Health, Boston, MA, USA
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| |
Collapse
|
12
|
Abstract
PURPOSE OF REVIEW Botswana, a small country in southern Africa, has had a very high prevalence of HIV since about 1995. It seems important to analyze the response of this country to help us understand how it became one of the first nations to achieve the 90-90-90 targets. RECENT FINDINGS Botswana began a national program for treatment of HIV/AIDS with ARVs in 2002. Initially established in the four largest population centers, it expanded to more than 30 sites throughout the country by 2004. Also in 2004, an 'opt out' system for HIV testing was introduced. The government-sponsored ARV regimen for initiation was ZDV/3TC/EFV until 2008, then TDF/FTC/EFV until 2016, when it became TDF/FTC/DTG along with the introduction of treatment for all. Levels of both acquired and transmitted drug resistance have been low. In late 2013, we began the Ya Tsie or Botswana Combination Prevention Project (BCCP), a cluster randomized trial for 100 000 exurban and rural adults in 30 villages that included enhanced testing, linkage to care, and ARV treatment for 15 intervention villages, one in each pair. A 20% baseline survey in 2013-2015 revealed 29% prevalence and values that were already close to 90-90-90. With 83.3% of HIV-positive adults knowing they were infected, 87.4% of those knowing they were infected already on ARV, and 96.5% of those on ARV in complete viral suppression, this represented a combined value of 70.2% toward the target of 73%. By best estimates, incidence fell by about 30% over the 29-month period of the trial, which is compatible with Botswana reaching a 90% reduction in incidence in 10 years as proposed by the UNAIDS model. On the basis of an end-of-study survey in three intervention villages, we estimate that Botswana could reach 95-95-95 by 2019. SUMMARY These results illustrate that it is possible to reach 90-90-90 in countries with very high HIV prevalence.
Collapse
|
13
|
Ajibola G, Rowley C, Maruapula D, Leidner J, Bennett K, Powis K, Shapiro RL, Lockman S. Drug resistance after cessation of efavirenz-based antiretroviral treatment started in pregnancy. South Afr J HIV Med 2020; 21:1023. [PMID: 32158555 PMCID: PMC7059240 DOI: 10.4102/sajhivmed.v21i1.1023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 09/16/2019] [Indexed: 01/11/2023] Open
Abstract
Background To reduce risk of antiretroviral resistance when stopping efavirenz (EFV)-based antiretroviral treatment (ART), staggered discontinuation of antiretrovirals (an NRTI tail) is recommended. However, no data directly support this recommendation. Objectives We evaluated the prevalence of HIV drug resistance mutations in pregnant women living with HIV who stopped efavirenz (EFV)/emtricitabine (FTC)/tenofovir disoproxil fumarate (TDF) postpartum. Method In accordance with the prevailing Botswana HIV guidelines at the time, women with pre-treatment CD4 > 350 cells/mm3, initiated EFV/FTC/TDF in pregnancy and stopped ART at 6 weeks postpartum if formula feeding, or 6 weeks after weaning. A 7-day tail of FTC/TDF was recommended per Botswana guidelines. HIV-1 RNA and genotypic resistance testing (bulk sequencing) were performed on samples obtained 4-6 weeks after stopping EFV. Stanford HIV Drug Resistance Database was used to identify major mutations. Results From April 2014 to May 2015, 74 women who had stopped EFV/FTC/TDF enrolled, with median nadir CD4 of 571 cells/mm3. The median time from cessation of EFV to sample draw for genotyping was 5 weeks (range: 3-13 weeks). Thirty-two (43%) women received a 1-week tail of FTC/TDF after stopping EFV. HIV-1 RNA was available from delivery in 70 (95%) women, 58 (83%) of whom had undetectable delivery HIV-1 RNA (< 40 copies/mL). HIV-1 RNA was available for 71 women at the time of genotyping, 45 (63%) of whom had HIV-1 RNA < 40 copies/mL. Thirty-five (47%) of 74 samples yielded a genotype result, and four (11%) had a major drug resistance mutation: two with K103N and two with V106M. All four resistance mutations occurred among women who did not receive an FTC/TDF tail (4/42, 10%), whereas no mutations occurred among 18 genotyped women who had received a 1-week FTC/TDF tail (p = 0.053). Conclusions Viral rebound was slow following cessation of EFV/FTC/TDF in the postpartum period. Use of an FTC/TDF tail after stopping EFV was associated with the lower prevalence of subsequent NNRTI drug resistance mutation.
Collapse
Affiliation(s)
- Globahan Ajibola
- Botswana Harvard T.H. Chan School of Public Health AIDS Initiative Partnership, Gaborone, Botswana
| | - Christopher Rowley
- Botswana Harvard T.H. Chan School of Public Health AIDS Initiative Partnership, Gaborone, Botswana.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, United States.,Beth Israel Deaconess Medical Center, Boston, United States
| | - Dorcas Maruapula
- Botswana Harvard T.H. Chan School of Public Health AIDS Initiative Partnership, Gaborone, Botswana
| | - Jean Leidner
- Goodtables Data Consulting, LLC., Norman, United States
| | - Kara Bennett
- Bennett Statistical Consulting, Inc., Ballston Lake, United States
| | - Kathleen Powis
- Botswana Harvard T.H. Chan School of Public Health AIDS Initiative Partnership, Gaborone, Botswana.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, United States.,Department of Medicine, Division of General Internal Medicine, Massachusetts General Hospital, Boston, United States.,Department of Pediatrics and Pediatric Surgery, Massachusetts General Hospital, Boston, United States
| | - Roger L Shapiro
- Botswana Harvard T.H. Chan School of Public Health AIDS Initiative Partnership, Gaborone, Botswana.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, United States.,Beth Israel Deaconess Medical Center, Boston, United States
| | - Shahin Lockman
- Botswana Harvard T.H. Chan School of Public Health AIDS Initiative Partnership, Gaborone, Botswana.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, United States.,Division of Infectious Disease, Brigham and Women's Hospital, Boston, United States
| |
Collapse
|
14
|
Seatla KK, Choga WT, Mogwele M, Diphoko T, Maruapula D, Mupfumi L, Musonda RM, Rowley CF, Avalos A, Kasvosve I, Moyo S, Gaseitsiwe S. Comparison of an in-house 'home-brew' and commercial ViroSeq integrase genotyping assays on HIV-1 subtype C samples. PLoS One 2019; 14:e0224292. [PMID: 31751353 PMCID: PMC6871785 DOI: 10.1371/journal.pone.0224292] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/09/2019] [Indexed: 12/22/2022] Open
Abstract
Background Roll-out of Integrase Strand Transfer Inhibitors (INSTIs) such as dolutegravir for HIV combination antiretroviral therapy (cART) in sub-Saharan Africa necessitates the development of affordable HIV drug resistance (HIVDR) assays targeting the Integrase gene. We optimised and evaluated an in-house integrase HIV-1 drug resistance assay (IH-Int) and compared it to a commercially available assay, ViroSeq™ Integrase Genotyping kit (VS-Int) amongst HIV-1 clade C infected individuals. Methods We used 54 plasma samples from treatment naïve participants and one plasma sample from a patient failing INSTI based cART. Specimens were genotyped using both the VS-Int and IH-Int assays. Stanford HIV drug resistance database were used for integrase resistance interpretation. We compared the major and minor resistance mutations, pairwise nucleotide and amino-acid identity, costs and assay time. Results Among 55 specimens tested with IH-Int, 53 (96.4%) successfully amplified compared to 45/55 (81.8%) for the VS-Int assay. The mean nucleotide and amino acid similarity from 33 paired sequences was 99.8% (SD ± 0.30) and 99.8% (SD ± 0.39) for the IH-Int and VS-Int assay respectively. The reagent cost/sample were 32 USD and 147 USD for IH-Int and VS-Int assay, respectively. All sequenced samples were confirmed as HIV-1 subtype C. Conclusions The IH-Int assay had a high amplification success rate and high concordance with the commercial assay. It is significantly cheaper compared to the commercial assay. Our assay has the needed specifications for routine monitoring of participants on Dolutegravir based regimens in Botswana.
Collapse
Affiliation(s)
- Kaelo K. Seatla
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Department of Medical Laboratory Sciences, School of Allied Health Professionals, University of Botswana, Gaborone, Botswana
| | - Wonderful T. Choga
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mompati Mogwele
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Department of Medical Laboratory Sciences, School of Allied Health Professionals, University of Botswana, Gaborone, Botswana
| | - Thabo Diphoko
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Department of Medical Laboratory Sciences, School of Allied Health Professionals, University of Botswana, Gaborone, Botswana
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Department of Medical Laboratory Sciences, School of Allied Health Professionals, University of Botswana, Gaborone, Botswana
| | - Lucy Mupfumi
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Department of Medical Laboratory Sciences, School of Allied Health Professionals, University of Botswana, Gaborone, Botswana
| | - Rosemary M. Musonda
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Christopher F. Rowley
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Ava Avalos
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Careena Centre for Health, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
| | - Ishmael Kasvosve
- Department of Medical Laboratory Sciences, School of Allied Health Professionals, University of Botswana, Gaborone, Botswana
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
15
|
Ndashimye E, Arts EJ. The urgent need for more potent antiretroviral therapy in low-income countries to achieve UNAIDS 90-90-90 and complete eradication of AIDS by 2030. Infect Dis Poverty 2019; 8:63. [PMID: 31370888 PMCID: PMC6676518 DOI: 10.1186/s40249-019-0573-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/28/2019] [Indexed: 12/17/2022] Open
Abstract
Background Over 90% of Human Immunodeficiency Virus (HIV) infected individuals will be on treatment by 2020 under UNAIDS 90–90-90 global targets. Under World Health Organisation (WHO) “Treat All” approach, this number will be approximately 36.4 million people with over 98% in low-income countries (LICs). Main body Pretreatment drug resistance (PDR) largely driven by frequently use of non-nucleoside reverse transcriptase inhibitors (NNRTIs), efavirenz and nevirapine, has been increasing with roll-out of combined antiretroviral therapy (cART) with 29% annual increase in some LICs countries. PDR has exceeded 10% in most LICs which warrants change of first line regimen to more robust classes under WHO recommendations. If no change in regimens is enforced in LICs, it’s estimated that over 16% of total deaths, 9% of new infections, and 8% of total cART costs will be contributed by HIV drug resistance by 2030. Less than optimal adherence, and adverse side effects associated with currently available drug regimens, all pose a great threat to achievement of 90% viral suppression and elimination of AIDS as a public health threat by 2030. This calls for urgent introduction of policies that advocate for voluntary and compulsory drug licensing of new more potent drugs which should also emphasize universal access of these drugs to all individuals worldwide. Conclusions The achievement of United Nations Programme on HIV and AIDS 2020 and 2030 targets in LICs depends on access to active cART with higher genetic barrier to drug resistance, better safety, and tolerability profiles. It’s also imperative to strengthen quality service delivery in terms of retention of patients to treatment, support for adherence to cART, patient follow up and adequate drug stocks to help achieve a free AIDS generation. Electronic supplementary material The online version of this article (10.1186/s40249-019-0573-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Emmanuel Ndashimye
- Department of Microbiology and Immunology, Western University, 1151 Richmond St., DSB Rm.3007, London, ON, N6A5C1, Canada. .,Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda.
| | - Eric J Arts
- Department of Microbiology and Immunology, Western University, 1151 Richmond St., DSB Rm.3007, London, ON, N6A5C1, Canada
| |
Collapse
|
16
|
Inzaule SC, Hamers RL, Bertagnolio S, Siedner MJ, Rinke de Wit TF, Gupta RK. Pretreatment HIV drug resistance in low- and middle-income countries. Future Virol 2019. [DOI: 10.2217/fvl-2018-0208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Pretreatment HIV drug resistance (PDR) has been increasing with scale-up of antiretroviral therapy (ART) in low- and middle-income countries. Delay in responding to rising levels of PDR is projected to fuel a worldwide increase in mortality, HIV incidence and ART costs. Strategies to curb the rise in PDR include using antiretrovirals (ARVs) with high-genetic barrier to resistance in first-line therapy and for prophylaxis in HIV exposed infants, enhancing HIV drug resistance surveillance in populations initiating, receiving ART, and in those on pre-exposure prophylaxis, universal access and effective use of viral-load tests, improving adherence and retention and minimizing ART programmatic quality gaps. In this review, we assess the drivers of PDR, and potential strategies to mitigate its rise in prevalence and impact in low- and middle-income countries.
Collapse
Affiliation(s)
- Seth C Inzaule
- Amsterdam Institute for Global Health & Development, Department of Global Health and Development, Amsterdam UMC, University of Amsterdam, 1105 BM, North Holland, The Netherlands
| | - Raph L Hamers
- Amsterdam Institute for Global Health & Development, Department of Global Health and Development, Amsterdam UMC, University of Amsterdam, 1105 BM, North Holland, The Netherlands
- Eijkman-Oxford Clinical Research Unit, and Faculty of Medicine Universitas Indonesia, Jalan Diponegoro 69, Jakarta, 10430, Indonesia
- Nuffield Department of Medicine, Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, OX3 7LF, UK
| | - Silvia Bertagnolio
- HIV/AIDS Department & Global Hepatitis Programme, World Health Organization, 20 avenue Appia, 1211 Geneva, 27, Switzerland
| | - Mark J Siedner
- Massachusetts General Hospital, Harvard University, 02114 Boston, MA, USA
- Department of Medicine, University of Cambridge, Cambridge, CB2 OXY, UK
| | - Tobias F Rinke de Wit
- Amsterdam Institute for Global Health & Development, Department of Global Health and Development, Amsterdam UMC, University of Amsterdam, 1105 BM, North Holland, The Netherlands
- Joep Lange Institute, 1105 BM, North Holland, The Netherlands
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, CB2 OXY, UK
- Africa Health Research Institute, 719 Umbilo Road, Durban, KZN, South Africa
| |
Collapse
|
17
|
Low rates of nucleoside reverse transcriptase inhibitor and nonnucleoside reverse transcriptase inhibitor drug resistance in Botswana. AIDS 2019; 33:1073-1082. [PMID: 30946161 PMCID: PMC6467559 DOI: 10.1097/qad.0000000000002166] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Supplemental Digital Content is available in the text Background: Scale-up of antiretroviral therapy (ART) and introduction of treat-all strategy necessitates population-level monitoring of acquired HIV drug resistance (ADR) and pretreatment drug resistance (PDR) mutations. Methods: Blood samples were collected from 4973 HIV-positive individuals residing in 30 communities across Botswana who participated in the Botswana Combination Prevention Project (BCPP) in 2013–2018. HIV sequences were obtained by long-range HIV genotyping. Major drug-resistance mutations (DRMs) and surveillance drug resistance mutations (SDRMs) associated with nucleoside reverse transcriptase inhibitors (NRTI) and nonnucleoside reverse transcriptase inhibitors (NNRTI) were analyzed according to the Stanford University HIV Drug Resistance Database. Viral sequences were screened for G-to-A hypermutations. A threshold of 2% was used for hypermutation adjustment. Viral suppression was considered at HIV-1 RNA load ≤400 copies/ml. Results: Among 4973 participants with HIV-1C sequences, ART data were available for 4927 (99%) including 3858 (78%) on ART. Among those on ART, 3435 had viral load data and 3297 (96%) were virologically suppressed. Among 1069 (22%) HIV-infected individuals not on ART, we found NRTI-associated and NNRTI-associated SDRMs were found in 1.5% (95% confidence interval [CI] 1.0–2.5%) and 2.9% (95% CI 2.0–4.2%), respectively. Of the 138 (4%) of individuals who had detectable HIV-1 RNA, we found NRTI-associated and NNRTI-associated drug resistance mutations in 16% (95% CI 10–25%) and 33% (95% CI 25–42%), respectively. Conclusion: We found a low prevalence of NRTI-associated and NNRTI-associated PDR-resistance mutations among residents of rural and peri-urban communities across Botswana. However, individuals on ART with detectable virus had ADR NRTI and NNRTI mutations above 15%.
Collapse
|
18
|
Rutstein SE, Chen JS, Nelson JAE, Phiri S, Miller WC, Hosseinipour MC. High rates of transmitted NNRTI resistance among persons with acute HIV infection in Malawi: implications for first-line dolutegravir scale-up. AIDS Res Ther 2019; 16:5. [PMID: 30795780 PMCID: PMC6385432 DOI: 10.1186/s12981-019-0220-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 02/07/2019] [Indexed: 11/10/2022] Open
Abstract
High rates of non-nucleoside reverse transcriptase inhibitors (NNRTI) resistance was a key consideration in the WHO policies transitioning first-line regimens to include integrase inhibitors (dolutegravir [DTG]). However, recent data suggests a relationship between DTG and neural tube defects among women exposed during conception, giving providers and policymakers pause regarding the planned regimen changes. We examined HIV drug resistance among a cohort of 46 acutely infected persons in Malawi. Our data demonstrates high levels of transmitted resistance, 11% using standard resistance surveillance mutations and 20% when additional NNRTI polymorphisms that may affect treatment response are included. High resistance rates in this treatment-naïve patient population reinforces the critical nature of DTG-based options in the context of public-health driven treatment programs.
Collapse
Affiliation(s)
- Sarah E. Rutstein
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC USA
| | - Jane S. Chen
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC USA
| | - Julie A. E. Nelson
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC USA
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC USA
| | | | | | - Mina C. Hosseinipour
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC USA
- UNC Project, Lilongwe, Malawi
| |
Collapse
|
19
|
Liu P, Liao L, Xu W, Yan J, Zuo Z, Leng X, Wang J, Kan W, You Y, Xing H, Ruan Y, Shao Y. Adherence, virological outcome, and drug resistance in Chinese HIV patients receiving first-line antiretroviral therapy from 2011 to 2015. Medicine (Baltimore) 2018; 97:e13555. [PMID: 30558015 PMCID: PMC6320000 DOI: 10.1097/md.0000000000013555] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Stavudine (D4T), zidovudine (AZT), and tenofovir (TDF) along with lamivudine (3TC) are the most widely used HIV treatment regimens in China. China's National Free Antiretroviral Treatment Programme (NFATP) has replaced D4T with AZT or TDF in the standard first-line regimens since 2010. Few studies have evaluated the adherence, virological outcome, and drug resistance in HIV patients receiving first-line antiretroviral therapy (ART) from 2011 to 2015 due to changes in ART regimen.From 2011 to 2015, 2787 HIV patients were examined, with 364, 1453, and 970 patients having initiated D4T-, AZT-, and TDF-based first-line ART regimens, respectively. The Cochran-Armitage test was used to examine the trends in clinical and virological outcomes during 2011 to 2015. Logistic regression was used to examine the effects of different regimens after 9 to 24 months of ART.From 2011 to 2014-2015, adverse drug reactions decreased from 18.9% to 6.7%, missed doses decreased from 9.9% to 4.6%, virological failure decreased from 16.2% to 6.4%, and drug resistance rates also significantly decreased from 5.4% to 1.1%. These successes were strongly associated with the standardized use of TDF- or AZT-based regimens in place of the D4T-based regimen. Poor adherence decreased from 11.3% in patients who initiated D4T-based regimens to 4.9% in those who initiated TDF-based regimens, adverse drug reactions decreased from 32.4% to 6.7%, virological failure reduced from 18.7% to 8.6%, and drug resistance reduced from 5.8% to 2.9%. Compared with patients who initiated AZT-based regimens, patients who initiated TDF-based regiments showed significant reductions in adherence issues, adverse drug reactions, virological outcomes, and drug resistance. Significant differences were also observed between those who initiated D4T- and AZT-based regimens.The good control of HIV replication and drug resistance was attributed to the success of China's NFATP from 2011 to 2015. This study provided real world evidence for further scaling up ART and minimizing the emergence of drug resistance in the "Three 90" era.
Collapse
Affiliation(s)
- Pengtao Liu
- Weifang Medical University, Weifang, Shandong Province
| | - Lingjie Liao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing
| | - Wei Xu
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing
| | - Jing Yan
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing
| | - Zhongbao Zuo
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing
| | - Xuebing Leng
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing
| | - Jing Wang
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing
| | - Wei Kan
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing
| | - Yinghui You
- Weifang Medical University, Weifang, Shandong Province
| | - Hui Xing
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing
| | - Yuhua Ruan
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing
- Guangxi Center for Disease Control and Prevention, Nanning, P. R. China
| | - Yiming Shao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing
- Guangxi Center for Disease Control and Prevention, Nanning, P. R. China
| |
Collapse
|
20
|
Abstract
BACKGROUND Resistance to antiretroviral therapy (ART) among people living with human immunodeficiency virus (HIV) compromises treatment effectiveness, often leading to virological failure and mortality. Antiretroviral drug resistance tests may be used at the time of initiation of therapy, or when treatment failure occurs, to inform the choice of ART regimen. Resistance tests (genotypic or phenotypic) are widely used in high-income countries, but not in resource-limited settings. This systematic review summarizes the relative merits of resistance testing in treatment-naive and treatment-exposed people living with HIV. OBJECTIVES To evaluate the effectiveness of antiretroviral resistance testing (genotypic or phenotypic) in reducing mortality and morbidity in HIV-positive people. SEARCH METHODS We attempted to identify all relevant studies, regardless of language or publication status, through searches of electronic databases and conference proceedings up to 26 January 2018. We searched MEDLINE, Embase, the Cochrane Central Register of Controlled Trials (CENTRAL), in the Cochrane Library, the World Health Organization (WHO) International Clinical Trials Registry Platform (ICTRP), and ClinicalTrials.gov to 26 January 2018. We searched Latin American and Caribbean Health Sciences Literature (LILACS) and the Web of Science for publications from 1996 to 26 January 2018. SELECTION CRITERIA We included all randomized controlled trials (RCTs) and observational studies that compared resistance testing to no resistance testing in people with HIV irrespective of their exposure to ART.Primary outcomes of interest were mortality and virological failure. Secondary outcomes were change in mean CD4-T-lymphocyte count, clinical progression to AIDS, development of a second or new opportunistic infection, change in viral load, and quality of life. DATA COLLECTION AND ANALYSIS Two review authors independently assessed each reference for prespecified inclusion criteria. Two review authors then independently extracted data from each included study using a standardized data extraction form. We analysed data on an intention-to-treat basis using a random-effects model. We performed subgroup analyses for the type of resistance test used (phenotypic or genotypic), use of expert advice to interpret resistance tests, and age (children and adolescents versus adults). We followed standard Cochrane methodological procedures. MAIN RESULTS Eleven RCTs (published between 1999 and 2006), which included 2531 participants, met our inclusion criteria. All of these trials exclusively enrolled patients who had previous exposure to ART. We found no observational studies. Length of follow-up time, study settings, and types of resistance testing varied greatly. Follow-up ranged from 12 to 150 weeks. All studies were conducted in Europe, USA, or South America. Seven studies used genotypic testing, two used phenotypic testing, and two used both phenotypic and genotypic testing. Only one study was funded by a manufacturer of resistance tests.Resistance testing made little or no difference in mortality (odds ratio (OR) 0.89, 95% confidence interval (CI) 0.36 to 2.22; 5 trials, 1140 participants; moderate-certainty evidence), and may have slightly reduced the number of people with virological failure (OR 0.70, 95% CI 0.56 to 0.87; 10 trials, 1728 participants; low-certainty evidence); and probably made little or no difference in change in CD4 cell count (mean difference (MD) -1.00 cells/mm³, 95% CI -12.49 to 10.50; 7 trials, 1349 participants; moderate-certainty evidence) or progression to AIDS (OR 0.64, 95% CI 0.31 to 1.29; 3 trials, 809 participants; moderate-certainty evidence). Resistance testing made little or no difference in adverse events (OR 0.89, 95% CI 0.51 to 1.55; 4 trials, 808 participants; low-certainty evidence) and probably reduced viral load (MD -0.23, 95% CI -0.35 to -0.11; 10 trials, 1837 participants; moderate-certainty evidence). No studies reported on development of new opportunistic infections or quality of life. We found no statistically significant heterogeneity for any outcomes, and the I² statistic value ranged from 0 to 25%. We found no subgroup effects for types of resistance testing (genotypic versus phenotypic), the addition of expert advice to interpretation of resistance tests, or age. Results for mortality were consistent when we compared studies at high or unclear risk of bias versus studies at low risk of bias. AUTHORS' CONCLUSIONS Resistance testing probably improved virological outcomes in people who have had virological failure in trials conducted 12 or more years ago. We found no evidence in treatment-naive people. Resistance testing did not demonstrate important patient benefits in terms of risk of death or progression to AIDS. The trials included very few participants from low- and middle-income countries.
Collapse
Affiliation(s)
- Theresa Aves
- McMaster UniversityDepartment of Health Research Methods, Evidence, and Impact1280 Main St WHamiltonOntarioCanadaL8S 4L8
| | - Joshua Tambe
- Yaoundé Central HospitalCentre for the Development of Best Practices in Health (CDBPH)YaoundéCameroon
| | - Reed AC Siemieniuk
- McMaster UniversityDepartment of Health Research Methods, Evidence, and Impact1280 Main St WHamiltonOntarioCanadaL8S 4L8
| | - Lawrence Mbuagbaw
- McMaster UniversityDepartment of Health Research Methods, Evidence, and Impact1280 Main St WHamiltonOntarioCanadaL8S 4L8
- Yaoundé Central HospitalCentre for the Development of Best Practices in Health (CDBPH)YaoundéCameroon
- South African Medical Research CouncilSouth African Cochrane CentreTygerbergSouth Africa
| | | |
Collapse
|
21
|
Etoori D, Ciglenecki I, Ndlangamandla M, Edwards CG, Jobanputra K, Pasipamire M, Maphalala G, Yang C, Zabsonre I, Kabore SM, Goiri J, Teck R, Kerschberger B. Successes and challenges in optimizing the viral load cascade to improve antiretroviral therapy adherence and rationalize second-line switches in Swaziland. J Int AIDS Soc 2018; 21:e25194. [PMID: 30350392 PMCID: PMC6198167 DOI: 10.1002/jia2.25194] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 09/26/2018] [Indexed: 11/11/2022] Open
Abstract
INTRODUCTION As antiretroviral therapy (ART) is scaled up, more patients become eligible for routine viral load (VL) monitoring, the most important tool for monitoring ART efficacy. For HIV programmes to become effective, leakages along the VL cascade need to be minimized and treatment switching needs to be optimized. However, many HIV programmes in resource-constrained settings report significant shortfalls. METHODS From a public sector HIV programme in rural Swaziland, we evaluated the VL cascade of adults (≥18 years) on ART from the time of the first elevated VL (>1000 copies/mL) between January 2013 and June 2014 to treatment switching by December 2015. We additionally described HIV drug resistance for patients with virological failure. We used descriptive statistics and Kaplan-Meier estimates to describe the different steps along the cascade and regression models to determine factors associated with outcomes. RESULTS AND DISCUSSION Of 828 patients with a first elevated VL, 252 (30.4%) did not receive any enhanced adherence counselling (EAC). Six hundred and ninety-six (84.1%) patients had a follow-up VL measurement, and the predictors of receiving a follow-up VL were being a second-line patient (adjusted hazard ratio (aHR): 0.72; p = 0.051), Hlathikhulu health zone (aHR: 0.79; p = 0.013) and having received two EAC sessions (aHR: 1.31; p = 0.023). Four hundred and ten patients (58.9%) achieved VL re-suppression. Predictors of re-suppression were age 50 to 64 (adjusted odds ratio (aOR): 2.02; p = 0.015) compared with age 18 to 34 years, being on second-line treatment (aOR: 3.29; p = 0.003) and two (aOR: 1.66; p = 0.045) or three (aOR: 1.86; p = 0.003) EAC sessions. Of 278 patients eligible to switch to second-line therapy, 120 (43.2%) had switched by the end of the study. Finally, of 155 successfully sequenced dried blood spots, 144 (92.9%) were from first-line patients. Of these, 133 (positive predictive value: 92.4%) had resistance patterns that necessitated treatment switching. CONCLUSIONS Patients on ART with high VLs were more likely to re-suppress if they received EAC. Failure to re-suppress after counselling was predictive of genotypically confirmed resistance patterns requiring treatment switching. Delays in switching were significant despite the ability of the WHO algorithm to predict treatment failure. Despite significant progress in recent years, enhanced focus on quality care along the VL cascade in resource-limited settings is crucial.
Collapse
Affiliation(s)
- David Etoori
- Research DepartmentMédecins Sans FrontièresMbabaneSwaziland
- Department of Population HealthLondon School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Iza Ciglenecki
- Research DepartmentMédecins Sans FrontièresGenevaSwitzerland
| | | | | | | | | | - Gugu Maphalala
- Swaziland National Reference Laboratory (NRL)Ministry of HealthMbabaneSwaziland
| | - Chunfu Yang
- Division of Global HIV/AIDSThe Centre for Disease ControlAtlantaGAUSA
| | | | - Serge M Kabore
- Research DepartmentMédecins Sans FrontièresMbabaneSwaziland
| | - Javier Goiri
- Research DepartmentMédecins Sans FrontièresGenevaSwitzerland
| | - Roger Teck
- Research DepartmentMédecins Sans FrontièresGenevaSwitzerland
- South African Medical UnitMédecins Sans FrontièresCape TownSouth Africa
| | | |
Collapse
|
22
|
Stirrup OT, Dunn DT, Tostevin A, Sabin CA, Pozniak A, Asboe D, Cox A, Orkin C, Martin F, Cane P. Risk factors and outcomes for the Q151M and T69 insertion HIV-1 resistance mutations in historic UK data. AIDS Res Ther 2018; 15:11. [PMID: 29661246 PMCID: PMC5902836 DOI: 10.1186/s12981-018-0198-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/28/2018] [Indexed: 01/24/2023] Open
Abstract
Background The prevalence of HIV-1 resistance to antiretroviral therapies (ART) has declined in high-income countries over recent years, but drug resistance remains a substantial concern in many low and middle-income countries. The Q151M and T69 insertion (T69i) resistance mutations in the viral reverse transcriptase gene can reduce susceptibility to all nucleoside/tide analogue reverse transcriptase inhibitors, motivating the present study to investigate the risk factors and outcomes associated with these mutations. Methods We considered all data in the UK HIV Drug Resistance Database for blood samples obtained in the period 1997–2014. Where available, treatment history and patient outcomes were obtained through linkage to the UK Collaborative HIV Cohort study. A matched case–control approach was used to assess risk factors associated with the appearance of each of the mutations in ART-experienced patients, and survival analysis was used to investigate factors associated with viral suppression. A further analysis using matched controls was performed to investigate the impact of each mutation on survival. Results A total of 180 patients with Q151M mutation and 85 with T69i mutation were identified, almost entirely from before 2006. Occurrence of both the Q151M and T69i mutations was strongly associated with cumulative period of virological failure while on ART, and for Q151M there was a particular positive association with use of stavudine and negative association with use of boosted-protease inhibitors. Subsequent viral suppression was negatively associated with viral load at sequencing for both mutations, and for Q151M we found a negative association with didanosine use but a positive association with boosted-protease inhibitor use. The results obtained in these analyses were also consistent with potentially large associations with other drugs. Analyses were inconclusive regarding associations between the mutations and mortality, but mortality was high for patients with low CD4 at detection. Conclusions The Q151M and T69i resistance mutations are now very rare in the UK. Our results suggest that good outcomes are possible for people with these mutations. However, in this historic sample, viral load and CD4 at detection were important factors in determining prognosis. Electronic supplementary material The online version of this article (10.1186/s12981-018-0198-7) contains supplementary material, which is available to authorized users.
Collapse
|
23
|
Inzaule SC, Hamers RL, Calis J, Boerma R, Sigaloff K, Zeh C, Mugyenyi P, Akanmu S, Rinke de Wit TF. When prevention of mother-to-child HIV transmission fails: preventing pretreatment drug resistance in African children. AIDS 2018; 32:143-147. [PMID: 29135578 DOI: 10.1097/qad.0000000000001696] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
24
|
Phillips AN, Cambiano V, Nakagawa F, Revill P, Jordan MR, Hallett TB, Doherty M, De Luca A, Lundgren JD, Mhangara M, Apollo T, Mellors J, Nichols B, Parikh U, Pillay D, Rinke de Wit T, Sigaloff K, Havlir D, Kuritzkes DR, Pozniak A, van de Vijver D, Vitoria M, Wainberg MA, Raizes E, Bertagnolio S. Cost-effectiveness of public-health policy options in the presence of pretreatment NNRTI drug resistance in sub-Saharan Africa: a modelling study. Lancet HIV 2017; 5:e146-e154. [PMID: 29174084 PMCID: PMC5843989 DOI: 10.1016/s2352-3018(17)30190-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/20/2017] [Accepted: 09/22/2017] [Indexed: 11/17/2022]
Abstract
Background There is concern over increasing prevalence of non-nucleoside reverse-transcriptase inhibitor (NNRTI) resistance in people initiating antiretroviral therapy (ART) in low-income and middle-income countries. We assessed the effectiveness and cost-effectiveness of alternative public health responses in countries in sub-Saharan Africa where the prevalence of pretreatment drug resistance to NNRTIs is high. Methods The HIV Synthesis Model is an individual-based simulation model of sexual HIV transmission, progression, and the effect of ART in adults, which is based on extensive published data sources and considers specific drugs and resistance mutations. We used this model to generate multiple setting scenarios mimicking those in sub-Saharan Africa and considered the prevalence of pretreatment NNRTI drug resistance in 2017. We then compared effectiveness and cost-effectiveness of alternative policy options. We took a 20 year time horizon, used a cost effectiveness threshold of US$500 per DALY averted, and discounted DALYs and costs at 3% per year. Findings A transition to use of a dolutegravir as a first-line regimen in all new ART initiators is the option predicted to produce the most health benefits, resulting in a reduction of about 1 death per year per 100 people on ART over the next 20 years in a situation in which more than 10% of ART initiators have NNRTI resistance. The negative effect on population health of postponing the transition to dolutegravir increases substantially with higher prevalence of HIV drug resistance to NNRTI in ART initiators. Because of the reduced risk of resistance acquisition with dolutegravir-based regimens and reduced use of expensive second-line boosted protease inhibitor regimens, this policy option is also predicted to lead to a reduction of overall programme cost. Interpretation A future transition from first-line regimens containing efavirenz to regimens containing dolutegravir formulations in adult ART initiators is predicted to be effective and cost-effective in low-income settings in sub-Saharan Africa at any prevalence of pre-ART NNRTI resistance. The urgency of the transition will depend largely on the country-specific prevalence of NNRTI resistance. Funding Bill & Melinda Gates Foundation, World Health Organization.
Collapse
Affiliation(s)
| | | | - Fumiyo Nakagawa
- Institute for Global Health, University College London, London, UK
| | | | | | | | | | | | - Jens D Lundgren
- Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Brooke Nichols
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
| | - Urvi Parikh
- University of Pittsburgh, Pittsburgh, PA, USA
| | - Deenan Pillay
- Africa Health Research Institute, KwaZulu Natal, South Africa; Division of Infection and Immunity, University College London, London, UK
| | | | - Kim Sigaloff
- Amsterdam Institute for Global Health & Development, San Francisco, CA, USA
| | - Diane Havlir
- University of California San Francisco, San Francisco, CA, USA
| | | | - Anton Pozniak
- Chelsea & Westminster Hospital NHS Trust, London, UK
| | | | | | | | - Elliot Raizes
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | |
Collapse
|
25
|
Pessôa R, Sanabani SS. High prevalence of HIV-1 transmitted drug-resistance mutations from proviral DNA massively parallel sequencing data of therapy-naïve chronically infected Brazilian blood donors. PLoS One 2017; 12:e0185559. [PMID: 28953964 PMCID: PMC5617215 DOI: 10.1371/journal.pone.0185559] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/14/2017] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND An improved understanding of the prevalence of low-abundance transmitted drug-resistance mutations (TDRM) in therapy-naïve HIV-1-infected patients may help determine which patients are the best candidates for therapy. In this study, we aimed to obtain a comprehensive picture of the evolving HIV-1 TDRM across the massive parallel sequences (MPS) of the viral entire proviral genome in a well-characterized Brazilian blood donor naïve to antiretroviral drugs. MATERIALS AND METHODS The MPS data from 128 samples used in the analysis were sourced from Brazilian blood donors and were previously classified by less-sensitive (LS) or "detuned" enzyme immunoassay as non-recent or longstanding HIV-1 infections. The Stanford HIV Resistance Database (HIVDBv 6.2) and IAS-USA mutation lists were used to interpret the pattern of drug resistance. The minority variants with TDRM were identified using a threshold of ≥ 1.0% and ≤ 20% of the reads sequenced. The rate of TDRM in the MPS data of the proviral genome were compared with the corresponding published consensus sequences of their plasma viruses. RESULTS No TDRM were detected in the integrase or envelope regions. The overall prevalence of TDRM in the protease (PR) and reverse transcriptase (RT) regions of the HIV-1 pol gene was 44.5% (57/128), including any mutations to the nucleoside analogue reverse transcriptase inhibitors (NRTI) and non-nucleoside analogue reverse transcriptase inhibitors (NNRTI). Of the 57 subjects, 43 (75.4%) harbored a minority variant containing at least one clinically relevant TDRM. Among the 43 subjects, 33 (76.7%) had detectable minority resistant variants to NRTIs, 6 (13.9%) to NNRTIs, and 16 (37.2%) to PR inhibitors. The comparison of viral sequences in both sources, plasma and cells, would have detected 48 DNA provirus disclosed TDRM by MPS previously missed by plasma bulk analysis. CONCLUSION Our findings revealed a high prevalence of TDRM found in this group, as the use of MPS drastically increased the detection of these mutations. Sequencing proviral DNA provided additional information about TDRM, which may impact treatment decisions. The overall results emphasize the importance of continuous monitoring.
Collapse
Affiliation(s)
- Rodrigo Pessôa
- Laboratory of Dermatology and Immunodeficiencies, Department of Dermatology, Tropical Medicine Institute of São Paulo, University of São Paulo, São Paulo, Brazil
| | - Sabri S. Sanabani
- Laboratory of Dermatology and Immunodeficiencies, Department of Dermatology, Tropical Medicine Institute of São Paulo, University of São Paulo, São Paulo, Brazil
- Clinical Laboratory, Department of Pathology, Hospital das Clínicas, School of Medicine, University of São Paulo, São Paulo, Brazil
- * E-mail:
| |
Collapse
|
26
|
Phillips AN, Stover J, Cambiano V, Nakagawa F, Jordan MR, Pillay D, Doherty M, Revill P, Bertagnolio S. Impact of HIV Drug Resistance on HIV/AIDS-Associated Mortality, New Infections, and Antiretroviral Therapy Program Costs in Sub-Saharan Africa. J Infect Dis 2017; 215:1362-1365. [PMID: 28329236 PMCID: PMC5451603 DOI: 10.1093/infdis/jix089] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 02/15/2017] [Indexed: 01/14/2023] Open
Abstract
To inform the level of attention to be given by antiretroviral therapy (ART) programs to HIV drug resistance (HIVDR), we used an individual-level model to estimate its impact on future AIDS deaths, HIV incidence, and ART program costs in sub–Saharan Africa (SSA) for a range of program situations. We applied this to SSA through the Spectrum-Goals model. In a situation in which current levels of pretreatment HIVDR are over 10% (mean, 15%), 16% of AIDS deaths (890 000 deaths), 9% of new infections (450 000), and 8% ($6.5 billion) of ART program costs in SSA in 2016–2030 will be attributable to HIVDR.
Collapse
Affiliation(s)
- Andrew N Phillips
- Institute for Global Health, University College London, United Kingdom
| | | | | | - Fumiyo Nakagawa
- Institute for Global Health, University College London, United Kingdom
| | | | - Deenan Pillay
- African Health Research Institute, KwaZulu-Natal, South Africa and Division of Infection and Immunity, University College London, United Kingdom
| | - Meg Doherty
- World Health Organisation, Geneva, Switzerland
| | - Paul Revill
- Centre for Health Economics, University of York, United Kingdom
| | | |
Collapse
|
27
|
Tambe J, Aves T, Siemieniuk R, Mbuagbaw L. Antiretroviral resistance testing in people living with HIV. Hippokratia 2017. [DOI: 10.1002/14651858.cd006495.pub4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Joshua Tambe
- Yaoundé Central Hospital; Centre for the Development of Best Practices in Health (CDBPH); Yaoundé Cameroon
| | - Theresa Aves
- McMaster University; Department of Health Research Methods, Evidence, and Impact; 1280 Main St W Hamilton Ontario Canada L8S 4L8
| | - Reed Siemieniuk
- McMaster University; Department of Health Research Methods, Evidence, and Impact; 1280 Main St W Hamilton Ontario Canada L8S 4L8
| | - Lawrence Mbuagbaw
- Yaoundé Central Hospital; Centre for the Development of Best Practices in Health (CDBPH); Yaoundé Cameroon
- McMaster University; Department of Health Research Methods, Evidence, and Impact; 1280 Main St W Hamilton Ontario Canada L8S 4L8
- South African Medical Research Council; South African Cochrane Centre; Tygerberg South Africa
| |
Collapse
|
28
|
Lavu E, Kave E, Mosoro E, Markby J, Aleksic E, Gare J, Elsum IA, Nano G, Kaima P, Dala N, Gurung A, Bertagnolio S, Crowe SM, Myatt M, Hearps AC, Jordan MR. High Levels of Transmitted HIV Drug Resistance in a Study in Papua New Guinea. PLoS One 2017; 12:e0170265. [PMID: 28146591 PMCID: PMC5287486 DOI: 10.1371/journal.pone.0170265] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/30/2016] [Indexed: 11/26/2022] Open
Abstract
Introduction Papua New Guinea is a Pacific Island nation of 7.3 million people with an estimated HIV prevalence of 0.8%. ART initiation and monitoring are guided by clinical staging and CD4 cell counts, when available. Little is known about levels of transmitted HIV drug resistance in recently infected individuals in Papua New Guinea. Methods Surveillance of transmitted HIV drug resistance in a total of 123 individuals recently infected with HIV and aged less than 30 years was implemented in Port Moresby (n = 62) and Mount Hagen (n = 61) during the period May 2013-April 2014. HIV drug resistance testing was performed using dried blood spots. Transmitted HIV drug resistance was defined by the presence of one or more drug resistance mutations as defined by the World Health Organization surveillance drug resistance mutations list. Results The prevalence of non-nucleoside reverse transcriptase inhibitor transmitted HIV drug resistance was 16.1% (95% CI 8.8%-27.4%) and 8.2% (95% CI 3.2%-18.2%) in Port Moresby and Mount Hagen, respectively. The prevalence of nucleoside reverse transcriptase inhibitor transmitted HIV drug resistance was 3.2% (95% CI 0.2%-11.7%) and 3.3% (95% CI 0.2%-11.8%) in Port Moresby and Mount Hagen, respectively. No protease inhibitor transmitted HIV drug resistance was observed. Conclusions The level of non-nucleoside reverse transcriptase inhibitor drug resistance in antiretroviral drug naïve individuals recently infected with HIV in Port Moresby is amongst the highest reported globally. This alarming level of transmitted HIV drug resistance in a young sexually active population threatens to limit the on-going effective use of NNRTIs as a component of first-line ART in Papua New Guinea. To support the choice of nationally recommended first-line antiretroviral therapy, representative surveillance of HIV drug resistance among antiretroviral therapy initiators in Papua New Guinea should be urgently implemented.
Collapse
Affiliation(s)
- Evelyn Lavu
- Central Public Health Laboratory, Port Moresby, Papua New Guinea
| | - Ellan Kave
- Central Public Health Laboratory, Port Moresby, Papua New Guinea
| | - Euodia Mosoro
- Central Public Health Laboratory, Port Moresby, Papua New Guinea
| | - Jessica Markby
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia
| | - Eman Aleksic
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia
| | - Janet Gare
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia
- Institute for Medical Research, Goroka, Papua New Guinea
| | - Imogen A. Elsum
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia
| | - Gideon Nano
- National Department of Health, Port Moresby, Papua New Guinea
| | | | - Nick Dala
- National Department of Health, Port Moresby, Papua New Guinea
| | - Anup Gurung
- World Health Organization, Port Moresby, Papua New Guinea
| | | | - Suzanne M. Crowe
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia
| | - Mark Myatt
- Brixton Health, Llawryglyn, Powys, Wales, United Kingdom
| | - Anna C. Hearps
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia
| | - Michael R. Jordan
- Division of Geographic Medicine and Infection Disease, Tufts Medical Center, Boston, Massachusetts, United States of America
- Tufts University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|