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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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Pagkrati I, Duke JL, Mbunwe E, Mosbruger TL, Ferriola D, Wasserman J, Dinou A, Tairis N, Damianos G, Kotsopoulou I, Papaioannou J, Giannopoulos D, Beggs W, Nyambo T, Mpoloka SW, Mokone GG, Njamnshi AK, Fokunang C, Woldemeskel D, Belay G, Maiers M, Tishkoff SA, Monos DS. Genomic characterization of HLA class I and class II genes in ethnically diverse sub-Saharan African populations: A report on novel HLA alleles. HLA 2023; 102:192-205. [PMID: 36999238 PMCID: PMC10524506 DOI: 10.1111/tan.15035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 03/11/2023] [Accepted: 03/11/2023] [Indexed: 04/01/2023]
Abstract
HLA allelic variation has been well studied and documented in many parts of the world. However, African populations have been relatively under-represented in studies of HLA variation. We have characterized HLA variation from 489 individuals belonging to 13 ethnically diverse populations from rural communities from the African countries of Botswana, Cameroon, Ethiopia, and Tanzania, known to practice traditional subsistence lifestyles using next generation sequencing (Illumina) and long-reads from Oxford Nanopore Technologies. We identified 342 distinct alleles among the 11 HLA targeted genes: HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, -DQA1, -DQB1, -DPA1, and -DPB1, with 140 of those alleles containing novel sequences that were submitted to the IPD-IMGT/HLA database. Sixteen of the 140 alleles contained novel content within the exonic regions of the genes, while 110 alleles contained novel intronic variants. Four alleles were found to be recombinants of already described HLA alleles and 10 alleles extended the sequence content of already described alleles. All 140 alleles include complete allelic sequence from the 5' UTR to the 3' UTR that are inclusive of all exons and introns. This report characterizes the HLA allelic variation from these individuals and describes the novel allelic variation present within these specific African populations.
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Affiliation(s)
- Ioanna Pagkrati
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Jamie L. Duke
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Eric Mbunwe
- Department of Genetics and Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Timothy L. Mosbruger
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Deborah Ferriola
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Jenna Wasserman
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Amalia Dinou
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Nikolaos Tairis
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Georgios Damianos
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Ioanna Kotsopoulou
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Joanna Papaioannou
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Diamantoula Giannopoulos
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - William Beggs
- Department of Genetics and Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Thomas Nyambo
- Department of Biochemistry, Kampala International University in Tanzania (KIUT), Dar es Salaam, Tanzania
| | - Sununguko W. Mpoloka
- Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | - Gaonyadiwe G. Mokone
- Department of Biomedical Sciences, Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | - Alfred K. Njamnshi
- Department of Neuroscience, Brain Research Africa Initiative (BRAIN), Yaoundé, Cameroon
- Department of Neurology & Neuroscience, Central Hospital Yaoundé, Yaoundé, Cameroon
- Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Charles Fokunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Dawit Woldemeskel
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gurja Belay
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Martin Maiers
- National Marrow Donor Program/Be The Match, Minneapolis, Minnesota, USA
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota, USA
| | - Sarah A. Tishkoff
- Department of Genetics and Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Dimitri S. Monos
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Modise BM, Mpoloka SW, Settypalli TBK, Hyera J, Natale A, Ceglie L, Gcebe N, Marobela-Raborokgwe C, Viljoen GJ, Cattoli G, Lamien CE. A novel multiplex qPCR‑HRM assay for the simultaneous detection of four abortive zoonotic agents in cattle, sheep, and goats. Sci Rep 2023; 13:12282. [PMID: 37507444 PMCID: PMC10382562 DOI: 10.1038/s41598-023-39447-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 07/25/2023] [Indexed: 07/30/2023] Open
Abstract
Abortifacient pathogens induce substantial economic losses in the livestock industry worldwide, and many of these pathogens are zoonotic, impacting human health. As Brucella spp., Coxiella burnetii, Leptospira spp., and Listeria monocytogenes cause abortion, rapid differential molecular diagnostic tests are needed to facilitate early and accurate detection of abortion to establish effective control measures. However, the available molecular methods are laborious, time-consuming, or costly. Therefore, we developed and validated a novel multiplex real-time polymerase chain reaction (qPCR) method based on high-resolution melting (HRM) curve analysis to simultaneously detect and differentiate four zoonotic abortifacient agents in cattle, goats, and sheep. Our HRM assay generated four well-separated melting peaks allowing the differentiation between the four zoonotic abortifacients. Out of 216 DNA samples tested, Brucella spp. was detected in 45 samples, Coxiella burnetii in 57 samples, Leptospira spp. in 12 samples, and Listeria monocytogenes in 19 samples, co-infection with Brucella spp. and Coxiella burnetii in 41 samples, and 42 samples were negative. This assay demonstrated good analytical sensitivity, specificity, and reproducibility. This is a valuable rapid, cost-saving, and reliable diagnostic tool for detecting individual and co-infections for zoonotic abortifacient agents in ruminants.
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Affiliation(s)
- Boitumelo M Modise
- Botswana National Veterinary Laboratory, Private Bag 0035, Gaborone, Botswana.
- Department of Biological Sciences, University of Botswana, Private Bag 00704, Gaborone, Botswana.
| | - Sununguko W Mpoloka
- Department of Biological Sciences, University of Botswana, Private Bag 00704, Gaborone, Botswana
| | - Tirumala B K Settypalli
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Wagramer Strasse 5, P.O. Box 100, 1400, Vienna, Austria
| | - Joseph Hyera
- Botswana Vaccine Institute, Private Bag 0031, Gaborone, Botswana
| | - Alda Natale
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viale dell'Università, 10, 35020, Legnaro, Italy
| | - Letizia Ceglie
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viale dell'Università, 10, 35020, Legnaro, Italy
| | - Nomakorinte Gcebe
- Agricultural Research Council-Bacteriology and Zoonotic Diseases Diagnostic Laboratory, Onderstepoort Veterinary Research, Pretoria, South Africa
| | | | - Gerrit J Viljoen
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Wagramer Strasse 5, P.O. Box 100, 1400, Vienna, Austria
| | - Giovanni Cattoli
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Wagramer Strasse 5, P.O. Box 100, 1400, Vienna, Austria
| | - Charles E Lamien
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Wagramer Strasse 5, P.O. Box 100, 1400, Vienna, Austria
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4
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.
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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 DOI: 10.1097/md.0000000000029577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [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.
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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
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6
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Kyobe S, Mwesigwa S, Kisitu GP, Farirai J, Katagirya E, Mirembe AN, Ketumile L, Wayengera M, Katabazi FA, Kigozi E, Wampande EM, Retshabile G, Mlotshwa BC, Williams L, Morapedi K, Kasvosve I, Kyosiimire-Lugemwa J, Nsangi B, Tsimako-Johnstone M, Brown CW, Joloba M, Anabwani G, Bhekumusa L, Mpoloka SW, Mardon G, Matshaba M, Kekitiinwa A, Hanchard NA. Exome Sequencing Reveals a Putative Role for HLA-C*03:02 in Control of HIV-1 in African Pediatric Populations. Front Genet 2021; 12:720213. [PMID: 34512729 PMCID: PMC8428176 DOI: 10.3389/fgene.2021.720213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/05/2021] [Indexed: 12/28/2022] Open
Abstract
Human leucocyte antigen (HLA) class I molecules present endogenously processed antigens to T-cells and have been linked to differences in HIV-1 disease progression. HLA allelotypes show considerable geographical and inter-individual variation, as does the rate of progression of HIV-1 disease, with long-term non-progression (LTNP) of disease having most evidence of an underlying genetic contribution. However, most genetic analyses of LTNP have occurred in adults of European ancestry, limiting the potential transferability of observed associations to diverse populations who carry the burden of disease. This is particularly true of HIV-1 infected children. Here, using exome sequencing (ES) to infer HLA allelotypes, we determine associations with HIV-1 LTNP in two diverse African pediatric populations. We performed a case-control association study of 394 LTNPs and 420 rapid progressors retrospectively identified from electronic medical records of pediatric HIV-1 populations in Uganda and Botswana. We utilized high-depth ES to perform high-resolution HLA allelotyping and assessed evidence of association between HLA class I alleles and LTNP. Sixteen HLA alleles and haplotypes had significantly different frequencies between Uganda and Botswana, with allelic differences being more prominent in HLA-A compared to HLA-B and C allelotypes. Three HLA allelotypes showed association with LTNP, including a novel association in HLA-C (HLA-B∗57:03, aOR 3.21, Pc = 0.0259; B∗58:01, aOR 1.89, Pc = 0.033; C∗03:02, aOR 4.74, Pc = 0.033). Together, these alleles convey an estimated population attributable risk (PAR) of non-progression of 16.5%. We also observed novel haplotype associations with HLA-B∗57:03-C∗07:01 (aOR 5.40, Pc = 0.025) and HLA-B∗58:01-C∗03:02 (aOR 4.88, Pc = 0.011) with a PAR of 9.8%, as well as a previously unreported independent additive effect and heterozygote advantage of HLA-C∗03:02 with B∗58:01 (aOR 4.15, Pc = 0.005) that appears to limit disease progression, despite weak LD (r 2 = 0.18) between these alleles. These associations remained irrespective of gender or country. In one of the largest studies of HIV in Africa, we find evidence of a protective effect of canonical HLA-B alleles and a novel HLA-C association that appears to augment existing HIV-1 control alleles in pediatric populations. Our findings outline the value of using multi-ethnic populations in genetic studies and offer a novel HIV-1 association of relevance to ongoing vaccine studies.
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Affiliation(s)
- Samuel Kyobe
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Savannah Mwesigwa
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Grace P. Kisitu
- Baylor College of Medicine Children’s Foundation, Kampala, Uganda
| | - John Farirai
- Botswana-Baylor Children’s Clinical Centre of Excellence, Gaborone, Botswana
| | - Eric Katagirya
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Lesego Ketumile
- Botswana-Baylor Children’s Clinical Centre of Excellence, Gaborone, Botswana
| | - Misaki Wayengera
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Fred Ashaba Katabazi
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Edgar Kigozi
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Edward M. Wampande
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gaone Retshabile
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Busisiwe C. Mlotshwa
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Lesedi Williams
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Koketso Morapedi
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Ishmael Kasvosve
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | | | - Betty Nsangi
- Baylor College of Medicine Children’s Foundation, Kampala, Uganda
| | | | - Chester W. Brown
- University of Tennessee Health Science Center, Memphis, TN, United States
| | - Moses Joloba
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gabriel Anabwani
- Botswana-Baylor Children’s Clinical Centre of Excellence, Gaborone, Botswana
| | - Lukhele Bhekumusa
- Eswatini - Baylor College of Medicine Children’s Foundation, Mbabane, Eswatini
| | - Sununguko W. Mpoloka
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Mogomotsi Matshaba
- Botswana-Baylor Children’s Clinical Centre of Excellence, Gaborone, Botswana
- Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Adeodata Kekitiinwa
- Baylor College of Medicine Children’s Foundation, Kampala, Uganda
- Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Neil A. Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
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Mbunwe E, Duke JL, Ferriola D, Mosbruger T, Damianos G, Dinou A, Kotsopoulou I, Ranciaro A, Thompson S, Beggs W, Mpoloka SW, Mokone GG, Nyambo T, Meskel DW, Belay G, Fokunang C, Njamnshi AK, Carrington M, Maiers M, Tishkoff S, Monos DS. P072 HLA types in ethnically diverse sub-saharan african populations. Hum Immunol 2019. [DOI: 10.1016/j.humimm.2019.07.125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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8
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Bajić V, Barbieri C, Hübner A, Güldemann T, Naumann C, Gerlach L, Berthold F, Nakagawa H, Mpoloka SW, Roewer L, Purps J, Stoneking M, Pakendorf B. Genetic structure and sex-biased gene flow in the history of southern African populations. Am J Phys Anthropol 2018; 167:656-671. [PMID: 30192370 PMCID: PMC6667921 DOI: 10.1002/ajpa.23694] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 07/13/2018] [Accepted: 07/15/2018] [Indexed: 12/31/2022]
Abstract
Objectives We investigated the genetic history of southern African populations with a special focus on their paternal history. We reexamined previous claims that the Y‐chromosome haplogroup E1b1b (E‐M293) was brought to southern Africa by pastoralists from eastern Africa, and investigated patterns of sex‐biased gene flow in southern Africa. Materials and methods We analyzed previously published complete mtDNA genome sequences and ∼900 kb of NRY sequences from 23 populations from Namibia, Botswana, and Zambia, as well as haplogroup frequencies from a large sample of southern African populations and 23 newly genotyped Y‐linked STR loci for samples assigned to haplogroup E1b1b. Results Our results support an eastern African origin for Y‐chromosome haplogroup E1b1b (E‐M293); however, its current distribution in southern Africa is not strongly associated with pastoralism, suggesting more complex demographic events and/or changes in subsistence practices in this region. The Bantu expansion in southern Africa had a notable genetic impact and was probably a rapid, male‐dominated expansion. Our finding of a significant increase in the intensity of the sex‐biased gene flow from north to south may reflect changes in the social dynamics between Khoisan and Bantu groups over time. Conclusions Our study shows that the population history of southern Africa has been complex, with different immigrating groups mixing to different degrees with the autochthonous populations. The Bantu expansion led to heavily sex‐biased admixture as a result of interactions between Khoisan females and Bantu males, with a geographic gradient which may reflect changes in the social dynamics between Khoisan and Bantu groups over time.
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Affiliation(s)
- Vladimir Bajić
- Department of Evolutionary Genetics, MPI for Evolutionary Anthropology, Leipzig, Germany
| | - Chiara Barbieri
- Department of Linguistic and Cultural Evolution, MPI for the Science of Human History, Jena, Germany.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Alexander Hübner
- Department of Evolutionary Genetics, MPI for Evolutionary Anthropology, Leipzig, Germany
| | - Tom Güldemann
- Department of Linguistic and Cultural Evolution, MPI for the Science of Human History, Jena, Germany.,Institute of Asian and African Studies, Humboldt University, Berlin, Germany
| | - Christfried Naumann
- Institute of Asian and African Studies, Humboldt University, Berlin, Germany
| | - Linda Gerlach
- Department of Human Behavior, Ecology and Culture, MPI for Evolutionary Anthropology, Leipzig, Germany
| | - Falko Berthold
- Max Planck Research Group on Comparative Population Linguistics, MPI for Evolutionary Anthropology, Leipzig, Germary
| | - Hirosi Nakagawa
- Institute of Global Studies, Tokyo University of Foreign Studies, Tokyo, Japan
| | - Sununguko W Mpoloka
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Lutz Roewer
- Charité - Universitätsmedizin Berlin, Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Berlin, Germany
| | - Josephine Purps
- Charité - Universitätsmedizin Berlin, Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Berlin, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, MPI for Evolutionary Anthropology, Leipzig, Germany
| | - Brigitte Pakendorf
- Laboratoire «Dynamique du Langage», CNRS & Université de Lyon, Lyon, France
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Mboowa G, Mwesigwa S, Katagirya E, Retshabile G, Mlotshwa BC, Williams L, Kekitiinwa A, Kateete D, Wampande E, Wayengera M, Kintu BN, Kisitu GP, Kyobe S, Brown CW, Hanchard NA, Mardon G, Joloba M, Anabwani G, Pettitt E, Tsimako-Johnstone M, Kasvosve I, Maplanka K, Mpoloka SW, Hlatshwayo M, Matshaba M. The Collaborative African Genomics Network (CAfGEN): Applying Genomic technologies to probe host factors important to the progression of HIV and HIV-tuberculosis infection in sub-Saharan Africa. AAS Open Res 2018; 1:3. [PMID: 30714022 PMCID: PMC6358002 DOI: 10.12688/aasopenres.12832.2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2018] [Indexed: 01/25/2023] Open
Abstract
Background: Here, we describe how the Collaborative African Genomics Network ( CAfGEN) of the Human Heredity and Health in Africa (H3Africa) consortium is using genomics to probe host genetic factors important to the progression of HIV and HIV-tuberculosis (TB) coinfection in sub-Saharan Africa. The H3Africa was conceived to facilitate the application of genomics technologies to improve health across Africa.. Methods: CAfGEN is an H3Africa collaborative centre comprising expertise from the University of Botswana; Makerere University; Baylor College of Medicine Children's Clinical Centers of Excellence (COEs) in Botswana, Uganda, and Swaziland; as well as Baylor College of Medicine, Texas. The COEs provide clinical expertise for community engagement, participant recruitment and sample collection while the three University settings facilitate processing and management of genomic samples and provide infrastructure and training opportunities to sustain genomics research. Results: The project has focused on utilizing whole-exome sequencing to identify genetic variants contributing to extreme HIV disease progression phenotypes in children, as well as RNA sequencing and integrated genomics to identify host genetic factors associated with TB disease progression among HIV-positive children. These cohorts, developed using the COEs' electronic medical records, are exceptionally well-phenotyped and present an unprecedented opportunity to assess genetic factors in individuals whose HIV was acquired by a different route than their adult counterparts in the context of a unique clinical course and disease pathophysiology. Conclusions: Our approach offers the prospect of developing a critical mass of well-trained, highly-skilled, continent-based African genomic scientists. To ensure long term genomics research sustainability in Africa, CAfGEN contributes to a wide range of genomics capacity and infrastructure development on the continent, has laid a foundation for genomics graduate programs at its institutions, and continues to actively promote genomics research through innovative forms of community engagement brokered by partnerships with governments and academia to support genomics policy formulation.
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Affiliation(s)
- Gerald Mboowa
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Savannah Mwesigwa
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Eric Katagirya
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gaone Retshabile
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | - Busisiwe C Mlotshwa
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | - Lesedi Williams
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | | | - David Kateete
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Eddie Wampande
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Bio-molecular Resources, College of Veterinary Medicine, Makerere University, Kampala, Uganda
| | - Misaki Wayengera
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Betty Nsangi Kintu
- Baylor College of Medicine Children's Foundation-Uganda, Kampala, Uganda
| | - Grace P Kisitu
- Baylor College of Medicine Children's Foundation-Uganda, Kampala, Uganda
| | - Samuel Kyobe
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Chester W Brown
- Genetics Division, Department of Pediatrics , University of Tennessee Health Science Center, Memphis, Memphis, TN, USA.,Le Bonheur Children's Hospital, Memphis, Memphis, TN, USA.,St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,ARS/USDA/Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine , Houston, TX, USA
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Moses Joloba
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gabriel Anabwani
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana.,Baylor College of Medicine Children's Foundation-Swaziland, Mbabane, Swaziland
| | - Ed Pettitt
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
| | - Masego Tsimako-Johnstone
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | - Ishmael Kasvosve
- Department of Medical Laboratory Sciences, University of Botswana, Gaborone, Botswana
| | - Koketso Maplanka
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | - Sununguko W Mpoloka
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | | | - Mogomotsi Matshaba
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana.,Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
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10
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Retshabile G, Mlotshwa BC, Williams L, Mwesigwa S, Mboowa G, Huang Z, Rustagi N, Swaminathan S, Katagirya E, Kyobe S, Wayengera M, Kisitu GP, Kateete DP, Wampande EM, Maplanka K, Kasvosve I, Pettitt ED, Matshaba M, Nsangi B, Marape M, Tsimako-Johnstone M, Brown CW, Yu F, Kekitiinwa A, Joloba M, Mpoloka SW, Mardon G, Anabwani G, Hanchard NA. Whole-Exome Sequencing Reveals Uncaptured Variation and Distinct Ancestry in the Southern African Population of Botswana. Am J Hum Genet 2018; 102:731-743. [PMID: 29706352 DOI: 10.1016/j.ajhg.2018.03.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/26/2018] [Indexed: 01/08/2023] Open
Abstract
Large-scale, population-based genomic studies have provided a context for modern medical genetics. Among such studies, however, African populations have remained relatively underrepresented. The breadth of genetic diversity across the African continent argues for an exploration of local genomic context to facilitate burgeoning disease mapping studies in Africa. We sought to characterize genetic variation and to assess population substructure within a cohort of HIV-positive children from Botswana-a Southern African country that is regionally underrepresented in genomic databases. Using whole-exome sequencing data from 164 Batswana and comparisons with 150 similarly sequenced HIV-positive Ugandan children, we found that 13%-25% of variation observed among Batswana was not captured by public databases. Uncaptured variants were significantly enriched (p = 2.2 × 10-16) for coding variants with minor allele frequencies between 1% and 5% and included predicted-damaging non-synonymous variants. Among variants found in public databases, corresponding allele frequencies varied widely, with Botswana having significantly higher allele frequencies among rare (<1%) pathogenic and damaging variants. Batswana clustered with other Southern African populations, but distinctly from 1000 Genomes African populations, and had limited evidence for admixture with extra-continental ancestries. We also observed a surprising lack of genetic substructure in Botswana, despite multiple tribal ethnicities and language groups, alongside a higher degree of relatedness than purported founder populations from the 1000 Genomes project. Our observations reveal a complex, but distinct, ancestral history and genomic architecture among Batswana and suggest that disease mapping within similar Southern African populations will require a deeper repository of genetic variation and allelic dependencies than presently exists.
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Affiliation(s)
- Gaone Retshabile
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Busisiwe C Mlotshwa
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Lesedi Williams
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Savannah Mwesigwa
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gerald Mboowa
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda; Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Zhuoyi Huang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Navin Rustagi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shanker Swaminathan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Katagirya
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Samuel Kyobe
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Misaki Wayengera
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Grace P Kisitu
- Baylor College of Medicine Children's Foundation, Kampala, Uganda
| | - David P Kateete
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda; Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Eddie M Wampande
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda; Department of Bio-molecular Resources, College of Veterinary Medicine, Makerere University, Kampala, Uganda
| | - Koketso Maplanka
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Ishmael Kasvosve
- Department of Medical Laboratory Sciences, University of Botswana, Gaborone, Botswana
| | - Edward D Pettitt
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
| | - Mogomotsi Matshaba
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana; Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Betty Nsangi
- Baylor College of Medicine Children's Foundation, Kampala, Uganda
| | - Marape Marape
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
| | | | - Chester W Brown
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; University of Tennessee Health Science Center, Memphis, TN 38105, USA
| | - Fuli Yu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Adeodata Kekitiinwa
- Baylor College of Medicine Children's Foundation, Kampala, Uganda; Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Moses Joloba
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Sununguko W Mpoloka
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gabriel Anabwani
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana; Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX 77030, USA.
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11
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Mboowa G, Mwesigwa S, Katagirya E, Retshabile G, Mlotshwa BC, Williams L, Kekitiinwa A, Kateete D, Wampande E, Wayengera M, Kintu BN, Kisitu GP, Kyobe S, Brown CW, Hanchard NA, Mardon G, Joloba M, Anabwani G, Pettitt E, Tsimako-Johnstone M, Kasvosve I, Maplanka K, Mpoloka SW, Hlatshwayo M, Matshaba M. The Collaborative African Genomics Network (CAfGEN): Applying Genomic technologies to probe host factors important to the progression of HIV and HIV-tuberculosis infection in sub-Saharan Africa. AAS Open Res 2018; 1:3. [DOI: 10.12688/aasopenres.12832.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Background: The Human Heredity and Health in Africa consortium (H3Africa) was conceived to facilitate the application of genomics technologies to improve health across Africa. Here, we describe how the Collaborative African Genomics Network (CAfGEN) of the H3Africa consortium is using genomics to probe host genetic factors important to the progression of HIV and HIV-tuberculosis (TB) coinfection in sub-Saharan Africa. Methods: CAfGEN is an H3Africa collaborative centre comprising expertise from the University of Botswana; Makerere University; Baylor College of Medicine Children’s Clinical Centers of Excellence (COEs) in Botswana, Uganda, and Swaziland; as well as Baylor College of Medicine, Texas. The COEs provide clinical expertise for community engagement, participant recruitment and sample collection while the three University settings facilitate processing and management of genomic samples and provide infrastructure and training opportunities to sustain genomics research. Results: The project has focused on utilizing whole-exome sequencing to identify genetic variants contributing to extreme HIV disease progression phenotypes in children, as well as RNA sequencing and integrated genomics to identify host genetic factors associated with TB disease progression among HIV-positive children. These cohorts, developed using the COEs’ electronic medical records, are exceptionally well-phenotyped and present an unprecedented opportunity to assess genetic factors in individuals whose HIV was acquired by a different route than their adult counterparts in the context of a unique clinical course and disease pathophysiology. Conclusions: Our approach offers the prospect of developing a critical mass of well-trained, highly-skilled, continent-based African genomic scientists. To ensure long term genomics research sustainability in Africa, CAfGEN contributes to a wide range of genomics capacity and infrastructure development on the continent, has laid a foundation for genomics graduate programs at its institutions, and continues to actively promote genomics research through innovative forms of community engagement brokered by partnerships with governments and academia to support genomics policy formulation.
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12
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Mlotshwa BC, Mwesigwa S, Mboowa G, Williams L, Retshabile G, Kekitiinwa A, Wayengera M, Kyobe S, Brown CW, Hanchard NA, Mardon G, Joloba M, Anabwani G, Mpoloka SW. The collaborative African genomics network training program: a trainee perspective on training the next generation of African scientists. Genet Med 2017; 19:826-833. [PMID: 28383545 PMCID: PMC5509501 DOI: 10.1038/gim.2016.177] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 09/19/2016] [Indexed: 11/09/2022] Open
Abstract
Purpose: The Collaborative African Genomics Network (CAfGEN) aims to establish sustainable genomics research programs in Botswana and Uganda through long-term training of PhD students from these countries at Baylor College of Medicine. Here, we present an overview of the CAfGEN PhD training program alongside trainees’ perspectives on their involvement. Background: Historically, collaborations between high-income countries (HICs) and low- and middle-income countries (LMICs), or North–South collaborations, have been criticized for the lack of a mutually beneficial distribution of resources and research findings, often undermining LMICs. CAfGEN plans to address this imbalance in the genomics field through a program of technology and expertise transfer to the participating LMICs. Methods: An overview of the training program is presented. Trainees from the CAfGEN project summarized their experiences, looking specifically at the training model, benefits of the program, challenges encountered relating to the cultural transition, and program outcomes after the first 2 years. Conclusion: Collaborative training programs like CAfGEN will not only help establish sustainable long-term research initiatives in LMICs but also foster stronger North–South and South–South networks. The CAfGEN model offers a framework for the development of training programs aimed at genomics education for those for whom genomics is not their “first language.” Genet Med advance online publication 06 April 2017
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Affiliation(s)
- Busisiwe C Mlotshwa
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | - Savannah Mwesigwa
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gerald Mboowa
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Lesedi Williams
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | - Gaone Retshabile
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | | | - Misaki Wayengera
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Samuel Kyobe
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Chester W Brown
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Current affiliation: Genetics Division, Department of Pediatrics, University of Tennessee Health Science Center, Le Bonheur Children's Hospital, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,ARS/USDA/Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030
| | - Moses Joloba
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gabriel Anabwani
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone
| | - Sununguko W Mpoloka
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
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Barbieri C, Güldemann T, Naumann C, Gerlach L, Berthold F, Nakagawa H, Mpoloka SW, Stoneking M, Pakendorf B. Unraveling the complex maternal history of Southern African Khoisan populations. Am J Phys Anthropol 2013; 153:435-48. [PMID: 24323467 DOI: 10.1002/ajpa.22441] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 11/12/2013] [Accepted: 11/15/2013] [Indexed: 02/03/2023]
Abstract
The Khoisan populations of southern Africa are known to harbor some of the deepest-rooting lineages of human mtDNA; however, their relationships are as yet poorly understood. Here, we report the results of analyses of complete mtDNA genome sequences from nearly 700 individuals representing 26 populations of southern Africa who speak diverse Khoisan and Bantu languages. Our data reveal a multilayered history of the indigenous populations of southern Africa, who are likely to be the result of admixture of different genetic substrates, such as resident forager populations and pre-Bantu pastoralists from East Africa. We find high levels of genetic differentiation of the Khoisan populations, which can be explained by the effect of drift together with a partial uxorilocal/multilocal residence pattern. Furthermore, there is evidence of extensive contact, not only between geographically proximate groups, but also across wider areas. The results of this contact, which may have played a role in the diffusion of common cultural and linguistic features, are especially evident in the Khoisan populations of the central Kalahari.
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Affiliation(s)
- Chiara Barbieri
- Max Planck Research Group on Comparative Population Linguistics, MPI for Evolutionary Anthropology, Leipzig, 04103, Germany
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