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Kyser AJ, Fotouh B, Mahmoud MY, Frieboes HB. Rising role of 3D-printing in delivery of therapeutics for infectious disease. J Control Release 2024; 366:349-365. [PMID: 38182058 PMCID: PMC10923108 DOI: 10.1016/j.jconrel.2023.12.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/18/2023] [Accepted: 12/28/2023] [Indexed: 01/07/2024]
Abstract
Modern drug delivery to tackle infectious disease has drawn close to personalizing medicine for specific patient populations. Challenges include antibiotic-resistant infections, healthcare associated infections, and customizing treatments for local patient populations. Recently, 3D-printing has become a facilitator for the development of personalized pharmaceutic drug delivery systems. With a variety of manufacturing techniques, 3D-printing offers advantages in drug delivery development for controlled, fine-tuned release and platforms for different routes of administration. This review summarizes 3D-printing techniques in pharmaceutics and drug delivery focusing on treating infectious diseases, and discusses the influence of 3D-printing design considerations on drug delivery platforms targeting these diseases. Additionally, applications of 3D-printing in infectious diseases are summarized, with the goal to provide insight into how future delivery innovations may benefit from 3D-printing to address the global challenges in infectious disease.
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Affiliation(s)
- Anthony J Kyser
- Department of Bioengineering, University of Louisville Speed School of Engineering, Louisville, KY 40202, USA.
| | - Bassam Fotouh
- Department of Bioengineering, University of Louisville Speed School of Engineering, Louisville, KY 40202, USA.
| | - Mohamed Y Mahmoud
- Department of Bioengineering, University of Louisville Speed School of Engineering, Louisville, KY 40202, USA; Department of Toxicology and Forensic Medicine, Faculty of Veterinary Medicine, Cairo University, Egypt.
| | - Hermann B Frieboes
- Department of Bioengineering, University of Louisville Speed School of Engineering, Louisville, KY 40202, USA; Center for Predictive Medicine, University of Louisville, Louisville, KY 40202, USA; Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY 40202, USA; UofL Health - Brown Cancer Center, University of Louisville, KY 40202, USA.
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Jeewanraj N, Mandizvo T, Mulaudzi T, Gumede N, Ndhlovu Z, Ndung'u T, Gounder K, Mann J. Partial compartmentalisation of HIV-1 subtype C between lymph nodes, peripheral blood mononuclear cells and plasma. Virology 2023; 582:62-70. [PMID: 37030154 PMCID: PMC10132742 DOI: 10.1016/j.virol.2023.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/10/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023]
Abstract
HIV-1 compartmentalisation is likely to have important implications for a preventative vaccine as well as eradication strategies. We genetically characterised HIV-1 subtype C variants in lymph nodes, peripheral blood mononuclear cells and plasma of six antiretroviral (ART) naïve individuals and four individuals on ART. Full-length env (n = 171) and gag (n = 250) sequences were generated from participants using single genome amplification. Phylogenetic relatedness of sequences was assessed, and compartmentalisation was determined using both distance and tree-based methods implemented in HyPhy. Additionally, potential associations between compartmentalisation and immune escape mutations were assessed. Partial viral compartmentalisation was present in nine of the ten participants. Broadly neutralising antibody (bnAb) escape was found to be associated with partial env compartmentalisation in some individuals, while cytotoxic T lymphocyte escape mutations in Gag were limited and did not differ between compartments. Viral compartmentalisation may be an important consideration for bnAb use in viral eradication.
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Affiliation(s)
- Neschika Jeewanraj
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Tawanda Mandizvo
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa; Africa Health Research Institute, Durban, South Africa
| | - Takalani Mulaudzi
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nombali Gumede
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Zaza Ndhlovu
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA; Division of Infection and Immunity, University College London, London, United Kingdom
| | - Kamini Gounder
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa; Africa Health Research Institute, Durban, South Africa
| | - Jaclyn Mann
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
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Webale SK, Kilongosi M, Munyekenye G, Onyango D, Marwa I, Bowen N. HIV-1 Transmission Cluster in Injection Drug Users in Nairobi City, Kenya. Ethiop J Health Sci 2023; 33:203-210. [PMID: 37484179 PMCID: PMC10358376 DOI: 10.4314/ejhs.v33i2.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/20/2022] [Indexed: 07/25/2023] Open
Abstract
Background While there is a striking increase in the prevalence of HIV in injection drug users, information on envelope-gene subtypes and transmission clusters in injection drug users is scarce. Method In a cross-sectional study, 247 injection drug users were recruited via out-rich method. Deoxyribonucleic acid was extracted from dry blood spot samples, amplified by Polymerase Chain Reaction and sequenced. Subtyping was performed using COntext-based Modeling for Expeditious Typing (COMET) and Recombinant Identification Program (RIP) tools. Phylogenetic diversity and Transmission clusters were identified using MEGA version 6.0 and TreeLink, respectively. Results Overall, 42 (17.0%) injection drug users were sero-positive for HIV-1. Of the 37 samples successfully sequenced, 29 (78.4%) sequences were identified as A1, 6 (16.2%) as AG while 1 (2.7%) as A1/G/AE and A1/C recombinants. The HIV subtypes formed clusters with little genetic diversity. Conclusion The high HIV prevalence was associated with transmission clusters and diversity in subtypes indicating ongoing local transmission. Therefore, there is need for comprehensive HIV care tailored to this population.
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Affiliation(s)
- Sella K Webale
- School of Biological sciences, Maseno University, Maseno, Kenya
| | - Mark Kilongosi
- School of Health Sciences, Kirinyaga University, Kutus, Kenya
| | | | - David Onyango
- School of Biological sciences, Maseno University, Maseno, Kenya
| | | | - Nancy Bowen
- National HIV Reference Laboratories, Ministry of Health, Nairobi city, Kenya
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Mwau M, Schaffer S, Kimani H, Kasiano P, Ogolla F, Ajema E, Adoyo S, Nyairo E, Saleri N, Nair SV. Comparison of the performance of Aptima HIV-1 Quant Dx Assay with Abbott RealTime HIV Assay for viral load monitoring using plasma and Dried Blood Spots collected in Kenya. PLoS One 2022; 17:e0269838. [PMID: 35994447 PMCID: PMC9394820 DOI: 10.1371/journal.pone.0269838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 05/28/2022] [Indexed: 11/28/2022] Open
Abstract
Introduction HIV-1 viral Load (VL) testing is recommended for the monitoring of antiretroviral treatment. Dried Blood Spots (DBS) are an effective sample type in resource limited settings, where safe phlebotomy and reliable shipping are hard to guarantee. In HIV high burden countries, high throughput assays can improve access to testing services. The Hologic Aptima HIV-1 Quant Dx Assay (Aptima Assay) is a high throughput assay that runs on the CE-IVD approved Panther platform. The objectives of this study were to assess the performance characteristics of Aptima for VL monitoring using plasma and venous DBS specimens and to determine the stability of HIV-1 RNA in DBS. Materials and methods This was a cross-sectional study of 2227 HIV infected adults visiting health facilities in Nairobi and Busia, Kenya. Each provided a venous blood sample; plasma was prepared from 1312 samples while paired DBS samples and plasma were prepared from the remaining 915 samples. The agreement between the Aptima assay and the Abbott RealTime HIV-1 Assay (Abbott RT) was analysed by comparing the HIV-1 VL in both assays at the medical decision point of 1000 copies/mL. To assess stability of HIV-1 RNA in DBS, VL in DBS spotted on day 0 were compared with that from the same DBS card after 21 days of storage at room temperature. Results Overall, 436 plasma samples had quantifiable results in both Aptima and Abbott RT. The agreement between the two assays at 1000 copies/mL was 97.48% with a Pearson’s correlation coefficient (r) of 0.9589 and gave a mean bias of 0.33 log copies/mL on Bland-Altman analysis. For fresh DBS, the agreement in both assays was 94.64% at 1000 copies/mL, with an r of 0.8692 and a mean bias of 0.35 log copies/mL. The overall agreement between DBS tested in Aptima on day 0 versus day 21 was 95.71%, with a mean bias of -0.154. Conclusion The Aptima HIV-1 Quant Dx assay is an accurate test for VL monitoring of HIV-1 using DBS and plasma sample types in Kenya.
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Affiliation(s)
- Matilu Mwau
- Kenya Medical Research Institute, Nairobi, Kenya
- * E-mail:
| | | | | | | | | | | | | | - Ednah Nyairo
- Kenya Medical Research Institute, Nairobi, Kenya
| | - Norah Saleri
- Kenya Medical Research Institute, Nairobi, Kenya
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Nduva GM, Otieno F, Kimani J, Wahome E, McKinnon LR, Cholette F, Majiwa M, Masika M, Mutua G, Anzala O, Graham SM, Gelmon L, Price MA, Smith AD, Bailey RC, Baele G, Lemey P, Hassan AS, Sanders EJ, Esbjörnsson J. Quantifying rates of HIV-1 flow between risk groups and geographic locations in Kenya: A country-wide phylogenetic study. Virus Evol 2022; 8:veac016. [PMID: 35356640 PMCID: PMC8962731 DOI: 10.1093/ve/veac016] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/23/2022] [Accepted: 03/01/2022] [Indexed: 12/14/2022] Open
Abstract
In Kenya, HIV-1 key populations including men having sex with men (MSM), people who inject drugs (PWID) and female sex workers (FSW) are thought to significantly contribute to HIV-1 transmission in the wider, mostly heterosexual (HET) HIV-1 transmission network. However, clear data on HIV-1 transmission dynamics within and between these groups are limited. We aimed to empirically quantify rates of HIV-1 flow between key populations and the HET population, as well as between different geographic regions to determine HIV-1 'hotspots' and their contribution to HIV-1 transmission in Kenya. We used maximum-likelihood phylogenetic and Bayesian inference to analyse 4058 HIV-1 pol sequences (representing 0.3 per cent of the epidemic in Kenya) sampled 1986-2019 from individuals of different risk groups and regions in Kenya. We found 89 per cent within-risk group transmission and 11 per cent mixing between risk groups, cyclic HIV-1 exchange between adjoining geographic provinces and strong evidence of HIV-1 dissemination from (i) West-to-East (i.e. higher-to-lower HIV-1 prevalence regions), and (ii) heterosexual-to-key populations. Low HIV-1 prevalence regions and key populations are sinks rather than major sources of HIV-1 transmission in Kenya. Targeting key populations in Kenya needs to occur concurrently with strengthening interventions in the general epidemic.
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Affiliation(s)
- George M Nduva
- Department of Translational Medicine, Lund University, Faculty of Medicine, Lund University, Box 117 SE-221 00 Lund, Sweden
- Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
| | - Frederick Otieno
- Nyanza Reproductive Health Society, United Mall, P.O. Box 1764, Kisumu, Kenya
| | - Joshua Kimani
- Department of Medical Microbiology, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, University of Manitoba (Bannatyne campus), Winnipeg MB R3E 0J9, Canada
| | - Elizabeth Wahome
- Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
| | - Lyle R McKinnon
- Department of Medical Microbiology, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, University of Manitoba (Bannatyne campus), Winnipeg MB R3E 0J9, Canada
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Private Bag X7, Congella 4013, South Africa
| | - Francois Cholette
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, University of Manitoba (Bannatyne campus), Winnipeg MB R3E 0J9, Canada
- National Microbiology Laboratory at the JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, 745 Logan Avenue, Winnipeg, Canada
| | - Maxwell Majiwa
- Kenya Medical Research Institute/Center for Global Health Research, KEMRI-CGHR, P.O. Box 20778-00202, Kisumu, Kenya
| | - Moses Masika
- Faculty of Health Sciences 3RD Floor Wing B, KAVI Institute of Clinical Research, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
| | - Gaudensia Mutua
- Faculty of Health Sciences 3RD Floor Wing B, KAVI Institute of Clinical Research, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
| | - Omu Anzala
- Faculty of Health Sciences 3RD Floor Wing B, KAVI Institute of Clinical Research, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
| | - Susan M Graham
- Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
- Department of Epidemiology, University of Washington, Office of the Chair, UW Box # 351619, Seattle, DC, USA
| | - Larry Gelmon
- Department of Medical Microbiology, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, University of Manitoba (Bannatyne campus), Winnipeg MB R3E 0J9, Canada
| | - Matt A Price
- IAVI Global Headquarters, 125 Broad Street, 9th Floor, New York, NY 10004, USA
- Department of Epidemiology and Biostatistics, University of California, Mission Hall: Global Health & Clinical Sciences Building, 550 16th Street, 2nd Floor, San Francisco, CA 94158-2549, USA
| | - Adrian D Smith
- Nuffield Department of Medicine, The University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK
| | - Robert C Bailey
- Nyanza Reproductive Health Society, United Mall, P.O. Box 1764, Kisumu, Kenya
- Division of Epidemiology and Biostatistics, University of Illinois at Chicago, 1603 W Taylor St, Chicago, IL 60612, USA
| | - Guy Baele
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Evolutionary and Computational Virology, Rega-Herestraat 49-box 1040, Leuven 3000, Belgium
| | - Philippe Lemey
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Evolutionary and Computational Virology, Rega-Herestraat 49-box 1040, Leuven 3000, Belgium
| | - Amin S Hassan
- Department of Translational Medicine, Lund University, Faculty of Medicine, Lund University, Box 117 SE-221 00 Lund, Sweden
- Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
| | - Eduard J Sanders
- Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
- Nuffield Department of Medicine, The University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, Faculty of Medicine, Lund University, Box 117 SE-221 00 Lund, Sweden
- Nuffield Department of Medicine, The University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK
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Mwau M, Danda J, Mbugua J, Handa A, Fortunko J, Worlock A, Nair SV. Prospective evaluation of accuracy of HIV viral load monitoring using the Aptima HIV Quant Dx assay with fingerstick and venous dried blood spots prepared under field conditions in Kenya. PLoS One 2021; 16:e0249376. [PMID: 33798221 PMCID: PMC8018649 DOI: 10.1371/journal.pone.0249376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 03/16/2021] [Indexed: 11/27/2022] Open
Abstract
Quantification of HIV-1 RNA is essential for clinical management of HIV patients. The limited throughput and significant hands-on time required by most HIV Viral load (VL) tests makes it challenging for laboratories with high test volume, to turn around patient results quickly. The Hologic Aptima HIV-1 Quant Dx Assay (Aptima), has the potential to alleviate this burden as it is high throughput and fully automated. This assay is validated for both plasma and dried blood spots (DBS), which are commonly used in resource limited settings. The objective of this study was to compare the performance of Aptima to Abbott RealTime HIV-1 Assay (Abbott RT), which was used as reference. This was a cross-sectional prospective study where HIV VL in finger stick (FS) DBS, venous blood (VB) DBS and plasma, collected from 258 consenting adults visiting 5 medical facilities in Kenya, Africa were tested in Aptima. The results were compared to plasma VL in Abbott RT at the medical decision point (MDP) of 1000 copies/mL and across Aptima assay range. The total agreement at MDP between plasma HIV VL in Abbott RT and plasma, FS and VB DBS tested in Aptima were 97.7%, 92.2% and 95.3% respectively with kappa statistic of 0.95, 0.84 and 0.90. The positive and negative agreement for all 3 sample types were >92%. Regression analysis between VL in Abbott RT plasma and various sample types tested in Aptima had a Pearson's correlation coefficient ≥0.91 with systematic bias of < 0.20 log copies/mL on Bland-Altman analysis. The high level of agreement in Aptima HIV VL results for all 3 sample types with Abbott RT plasma VL along with the high throughput, complete automation, and ease of use of the Panther platform makes Aptima a good option for HIV VL monitoring for busy laboratories with high volume of testing.
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Affiliation(s)
- Matilu Mwau
- Kenya Medical Research Institute, Nairobi, Kenya
| | - Jeff Danda
- Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Allan Handa
- Kenya Medical Research Institute, Nairobi, Kenya
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Nduva GM, Hassan AS, Nazziwa J, Graham SM, Esbjörnsson J, Sanders EJ. HIV-1 Transmission Patterns Within and Between Risk Groups in Coastal Kenya. Sci Rep 2020; 10:6775. [PMID: 32317722 PMCID: PMC7174422 DOI: 10.1038/s41598-020-63731-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/30/2020] [Indexed: 11/09/2022] Open
Abstract
HIV-1 transmission patterns within and between populations at different risk of HIV-1 acquisition in Kenya are not well understood. We investigated HIV-1 transmission networks in men who have sex with men (MSM), injecting drug users (IDU), female sex workers (FSW) and heterosexuals (HET) in coastal Kenya. We used maximum-likelihood and Bayesian phylogenetics to analyse new (N = 163) and previously published (N = 495) HIV-1 polymerase sequences collected during 2005-2019. Of the 658 sequences, 131 (20%) were from MSM, 58 (9%) IDU, 109 (17%) FSW, and 360 (55%) HET. Overall, 206 (31%) sequences formed 61 clusters. Most clusters (85%) consisted of sequences from the same risk group, suggesting frequent within-group transmission. The remaining clusters were mixed between HET/MSM (7%), HET/FSW (5%), and MSM/FSW (3%) sequences. One large IDU-exclusive cluster was found, indicating an independent sub-epidemic among this group. Phylodynamic analysis of this cluster revealed a steady increase in HIV-1 infections among IDU since the estimated origin of the cluster in 1987. Our results suggest mixing between high-risk groups and heterosexual populations and could be relevant for the development of targeted HIV-1 prevention programmes in coastal Kenya.
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Affiliation(s)
- George M Nduva
- Lund University, Lund, Sweden
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
| | - Amin S Hassan
- Lund University, Lund, Sweden
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Susan M Graham
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- University of Washington, Seattle, WA, USA
| | - Joakim Esbjörnsson
- Lund University, Lund, Sweden.
- The University of Oxford, Oxford, United Kingdom.
| | - Eduard J Sanders
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- The University of Oxford, Oxford, United Kingdom
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Abstract
PURPOSE OF REVIEW To provide a summary of the current data on the global HIV subtype diversity and distribution by region. HIV is one of the most genetically diverse pathogens due to its high-mutation and recombination rates, large population size and rapid replication rate. This rapid evolutionary process has resulted in several HIV subtypes that are heterogeneously globally distributed. RECENT FINDINGS Subtype A remains the most prevalent strain in parts of East Africa, Russia and former Soviet Union countries; subtype B in Europe, Americas and Oceania; subtype C in Southern Africa and India; CRF01_AE in Asia and CRF02_AG in Western Africa. Recent studies based on near full-length genome sequencing highlighted the growing importance of recombinant variants and subtype C viruses. SUMMARY The dynamic change in HIV subtype distribution presents future challenges for diagnosis, treatment and vaccine design and development. An increase in recombinant viruses suggests that coinfection and superinfection by divergent HIV strains has become more common necessitating continuous surveillance to keep track of the viral diversity. Cheaper near full-length genome sequencing approaches are critical in improving HIV subtype estimations. However, missing subtype data and low sequence sampling levels are still a challenge in some geographical regions. VIDEO ABSTRACT: http://links.lww.com/COHA/A14.
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Hassan AS, Esbjörnsson J, Wahome E, Thiong’o A, Makau GN, Price MA, Sanders EJ. HIV-1 subtype diversity, transmission networks and transmitted drug resistance amongst acute and early infected MSM populations from Coastal Kenya. PLoS One 2018; 13:e0206177. [PMID: 30562356 PMCID: PMC6298690 DOI: 10.1371/journal.pone.0206177] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/08/2018] [Indexed: 11/21/2022] Open
Abstract
Background HIV-1 molecular epidemiology amongst men who have sex with men (MSM) in sub-Saharan Africa remains not well characterized. We aimed to determine HIV-1 subtype distribution, transmission clusters and transmitted drug resistance (TDR) in acute and early infected MSM from Coastal Kenya. Methods Analysis of HIV-1 partial pol sequences from MSM recruited 2005–2017 and sampled within six months of the estimated date of infection. Volunteers were classified as men who have sex with men exclusively (MSME) or with both men and women (MSMW). HIV-1 subtype and transmission clusters were determined by maximum-likelihood phylogenetics. TDR mutations were determined using the Stanford HIV drug resistance database. Results Of the 97 volunteers, majority (69%) were MSMW; 74%, 16%, 9% and 1% had HIV-1 subtypes A1, D, C or G, respectively. Overall, 65% formed transmission clusters, with substantial mixing between MSME and MSMW. Majority of volunteer sequences were either not linked to any reference sequence (56%) or clustered exclusively with sequences of Kenyan origin (19%). Eight (8% [95% CI: 4–16]) had at least one TDR mutation against nucleoside (n = 2 [2%]) and/or non-nucleoside (n = 7 [7%]) reverse transcriptase inhibitors. The most prevalent TDR mutation was K103N (n = 5), with sequences forming transmission clusters of two and three taxa each. There were no significant differences in HIV-1 subtype distribution and TDR between MSME and MSMW. Conclusions This HIV-1 MSM epidemic was predominantly sub-subtype A1, of Kenyan origin, with many transmission clusters and having intermediate level of TDR. Targeted HIV-1 prevention, early identification and care interventions are warranted to break the transmission cycle amongst MSM from Coastal Kenya.
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Affiliation(s)
- Amin S. Hassan
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Lund University, Lund, Sweden
- * E-mail:
| | | | | | | | - George N. Makau
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Lund University, Lund, Sweden
| | - Mathew A. Price
- International AIDS Vaccine Initiative, New York, New York, United States of America
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, California, United States of America
| | - Eduard J. Sanders
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Oxford University, Oxford, United Kingdom
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