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Ouedraogo AR, Traoré L, Ouattara AK, Ouedraogo AR, Zongo SV, Savadogo M, Lallogo TD, Sombie HK, Sorgho PA, Ouedraogo TWC, Djigma FW, Lamien AS, Yonli AT, Lompo OM, Simporé J. Association of HLA-DRB1*11 and HLA-DRB1*12 gene polymorphism with COVID-19 in Burkina Faso. BMC Med Genomics 2023; 16:246. [PMID: 37845715 PMCID: PMC10577973 DOI: 10.1186/s12920-023-01684-8] [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: 04/13/2023] [Accepted: 10/03/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND The clinical manifestations of coronavirus disease (COVID-19) can vary widely, ranging from asymptomatic to severe, and may be influenced by the host genetic background. The aim of the present study was to determine the frequencies of HLA-DRB1*11 and HLA-DRB1*12 allele polymorphisms and their associations with COVID-19. METHODS In this cross-sectional study, 198 subjects were enrolled, including 150 COVID-19 positive cases and 48 subjects who tested negative for COVID-19. Participants were recruited from the emergency, intensive care, and infectious diseases departments of the Bogodogo Centre University Hospital (CHU-B) or the routine laboratory of Centre de Recherche Biomoléculaire Pietro Annigoni (CERBA). Genomic DNA was extracted from nasopharyngeal swabs samples and multiplex PCR-SSP was used to detect the HLA-DRB1*11 and HLA-DRB1*12 alleles. The study was approved by CERS (№ 2021-02-033). RESULTS The positive cases were categorized into 38 asymptomatic (CC+), 60 symptomatic (NC+), and 52 severe cases (SC+). Females were more frequent in the overall study population (53.0%, 105/198) as well as in the negative group's CC- (68.75%, 33/48) and SC+ (57.69%, 30/52 negative groups, whereas males were more frequent in the CC+ (63.16%, 24/38) and NC+ (53.33%, 32/60) groups. The highest mean age was observed in the SC + group. A frequency of 19.19% (38/198) and 14.65% (29/198) was found for the HLA-DRB1*11 and HLA-DRB1*12 alleles, respectively. Individuals carrying the HLA-DRB1*11 allele had an approximately sixfold higher risk of asymptomatic SARS-CoV-2 infection (OR = 5.72 [1.683-19.442], p = 0.005) based on the association analysis. CONCLUSIONS Altogether, the present study reports high frequency of HLA-DRB1*11 and HLA-DRB1*12 alleles within a population from Ouagadougou, Burkina Faso. The results suggest that individuals carrying the HLA-DRB1*11 allele are more susceptible to COVID-19 infection but may not display symptoms.
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Affiliation(s)
- Alfred Rakissida Ouedraogo
- Laboratoire de Morphologie et Organogénèse (LAMO), Université Joseph KI-ZERBO, UFR/SDS, Ouagadougou 01, 01 BP 7021, Burkina Faso
| | - Lassina Traoré
- Université Joseph KI-ZERBO, Laboratoire de Biologie Moléculaire et de Génétique (LABIOGENE), UFR/SVT, Ouagadougou 01, 01 BP 7021, Burkina Faso
- Université Norbert ZONGO - Centre Universitaire de Manga, BP 376, Koudougou, Burkina Faso
| | - Abdoul Karim Ouattara
- Université Joseph KI-ZERBO, Laboratoire de Biologie Moléculaire et de Génétique (LABIOGENE), UFR/SVT, Ouagadougou 01, 01 BP 7021, Burkina Faso
- Université Norbert ZONGO - Centre Universitaire de Manga, BP 376, Koudougou, Burkina Faso
| | - Alexis Rakiswende Ouedraogo
- Laboratoire de Morphologie et Organogénèse (LAMO), Université Joseph KI-ZERBO, UFR/SDS, Ouagadougou 01, 01 BP 7021, Burkina Faso
| | - Sidnooma Véronique Zongo
- Université Joseph KI-ZERBO, Laboratoire de Biologie Moléculaire et de Génétique (LABIOGENE), UFR/SVT, Ouagadougou 01, 01 BP 7021, Burkina Faso
| | - Mousso Savadogo
- Université Joseph KI-ZERBO, Laboratoire de Biologie Moléculaire et de Génétique (LABIOGENE), UFR/SVT, Ouagadougou 01, 01 BP 7021, Burkina Faso
| | - Tatiana Doriane Lallogo
- Université Joseph KI-ZERBO, Laboratoire de Biologie Moléculaire et de Génétique (LABIOGENE), UFR/SVT, Ouagadougou 01, 01 BP 7021, Burkina Faso
| | - Herman Karim Sombie
- Centre de Recherche Biomoléculaire Pietro Annigoni (CERBA), P.O. Box 364, Ouagadougou 01, Burkina Faso
| | - Pegdwendé Abel Sorgho
- Université Joseph KI-ZERBO, Laboratoire de Biologie Moléculaire et de Génétique (LABIOGENE), UFR/SVT, Ouagadougou 01, 01 BP 7021, Burkina Faso
- Centre de Recherche Biomoléculaire Pietro Annigoni (CERBA), P.O. Box 364, Ouagadougou 01, Burkina Faso
| | - Teega-Wendé Clarisse Ouedraogo
- Université Joseph KI-ZERBO, Laboratoire de Biologie Moléculaire et de Génétique (LABIOGENE), UFR/SVT, Ouagadougou 01, 01 BP 7021, Burkina Faso
| | - Florencia Wendkuuni Djigma
- Université Joseph KI-ZERBO, Laboratoire de Biologie Moléculaire et de Génétique (LABIOGENE), UFR/SVT, Ouagadougou 01, 01 BP 7021, Burkina Faso.
| | - Assita Sanou Lamien
- Laboratoire de Morphologie et Organogénèse (LAMO), Université Joseph KI-ZERBO, UFR/SDS, Ouagadougou 01, 01 BP 7021, Burkina Faso
| | - Albert Théophane Yonli
- Centre de Recherche Biomoléculaire Pietro Annigoni (CERBA), P.O. Box 364, Ouagadougou 01, Burkina Faso
| | - Olga Mélanie Lompo
- Laboratoire de Morphologie et Organogénèse (LAMO), Université Joseph KI-ZERBO, UFR/SDS, Ouagadougou 01, 01 BP 7021, Burkina Faso
| | - Jacques Simporé
- Université Joseph KI-ZERBO, Laboratoire de Biologie Moléculaire et de Génétique (LABIOGENE), UFR/SVT, Ouagadougou 01, 01 BP 7021, Burkina Faso
- Centre de Recherche Biomoléculaire Pietro Annigoni (CERBA), P.O. Box 364, Ouagadougou 01, Burkina Faso
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Lallogo TD, Djigma FW, Sorgho PA, Martinson JJ, Rebeca Compaore T, Traore L, Bado P, Bapio Valérie Elvira Jean Télesphore Bazie, Amegnona LJ, Kagone TS, Alice Ouedraogo R, Ilboudo DP, Obiri-Yeboah D, Yonli AT, Simpore J. KIR2DL5B and HLA DRB1*12 alleles seems to be associated with protection against HIV-1 in serodiscordant couples in Burkina Faso. J Med Virol 2022; 94:4425-4432. [PMID: 35501290 DOI: 10.1002/jmv.27821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 11/05/2022]
Abstract
INTRODUCTION The Human Immunodeficiency Virus (HIV) belongs to the Retroviridae family and remains a public health problem in sub-Saharan Africa. Recent reports from WHO have shown that 33 million people died from HIV infections. HIV is one of the most serious fatal human diseases of the 20th and 21st centuries. However, variations in genetic and immunological factors are associated with protection against HIV infection in uninfected people exposed to HIV. This is the case with Naturals Killers which play an important role in the progression or regression of HIV infection. The objective of this study is to characterize certain HLA (Human Leukocyte Antigen) class II genes and KIR genes in HIV-1 serodiscordant couples in Burkina Faso. METHODS This study was carried out at Burkina Faso among nineteen (19) HIV-1 serodiscordant couples. Classical multiplex PCR (SSP-PCR) was used to characterize the presence or absence of the KIR genes and certain class II HLAs (DRB1*11 and DRB1*12). RESULTS The characterization of the KIR and HLA genes DRB1*11, DRB1*12 in this study demonstrated that the inhibitor KIR2DL5B, would confer protection against HIV-1 infection in seronegative partners [OR = 0.13 (0.02-0.72) and p = 0.029)], and the HLA DRB1*12 allele was associated with protection against HIV-1 infection in seronegative partners [OR = 0.16 (0.03-0.77) and p = 0.038]. AA and Bx haplotypes were not found to be associated with HIV-1 infection in serodiscordant couples. CONCLUSION This study confirms the involvement of the KIR genes in viral pathologies such as HIV-1 infection. Future larger-scale studies may provide a better understanding of the molecular mechanism by which the KIR Haplotype and combination of KIR/HLA are associated with protection against HIV infection. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Tatiana Doriane Lallogo
- Molecular Biology and Genetics Laboratory (LABIOGENE), Department of Biochemistry and Microbiology, University Joseph KI-ZERBO, PO Box 7021, Ouagadougou, 03, Burkina Faso
| | - Florencia W Djigma
- Molecular Biology and Genetics Laboratory (LABIOGENE), Department of Biochemistry and Microbiology, University Joseph KI-ZERBO, PO Box 7021, Ouagadougou, 03, Burkina Faso.,Pietro Annigoni Biomolecular Research Center (CERBA), PO Box 364, Ouagadougou, 01, Burkina Faso
| | - Pegdwendé Abel Sorgho
- Pietro Annigoni Biomolecular Research Center (CERBA), PO Box 364, Ouagadougou, 01, Burkina Faso
| | - Jeremy James Martinson
- Laboratory of Infectious Diseases/Microbiology, University of Pittsburgh, Pittsburgh, USA
| | - T Rebeca Compaore
- Institute for Research in Health Sciences, IRSS, Ouagadougou, Burkina Faso
| | - Lassina Traore
- Molecular Biology and Genetics Laboratory (LABIOGENE), Department of Biochemistry and Microbiology, University Joseph KI-ZERBO, PO Box 7021, Ouagadougou, 03, Burkina Faso
| | - Prosper Bado
- Molecular Biology and Genetics Laboratory (LABIOGENE), Department of Biochemistry and Microbiology, University Joseph KI-ZERBO, PO Box 7021, Ouagadougou, 03, Burkina Faso
| | | | - Lanyo Jospin Amegnona
- Molecular Biology and Genetics Laboratory (LABIOGENE), Department of Biochemistry and Microbiology, University Joseph KI-ZERBO, PO Box 7021, Ouagadougou, 03, Burkina Faso
| | - Thérèse S Kagone
- National Institute of Public Health, Center Muraz, 01 BP 390 Bobo-Dioulasso 01, Burkina Faso
| | - R Alice Ouedraogo
- Molecular Biology and Genetics Laboratory (LABIOGENE), Department of Biochemistry and Microbiology, University Joseph KI-ZERBO, PO Box 7021, Ouagadougou, 03, Burkina Faso
| | | | - Dorcas Obiri-Yeboah
- Department of Microbiology and Immunology, School of Medical Sciences, University of Cape Coast, PMB, Cape Coast, Ghana
| | - Albert Théophane Yonli
- Molecular Biology and Genetics Laboratory (LABIOGENE), Department of Biochemistry and Microbiology, University Joseph KI-ZERBO, PO Box 7021, Ouagadougou, 03, Burkina Faso.,Pietro Annigoni Biomolecular Research Center (CERBA), PO Box 364, Ouagadougou, 01, Burkina Faso
| | - Jacques Simpore
- Molecular Biology and Genetics Laboratory (LABIOGENE), Department of Biochemistry and Microbiology, University Joseph KI-ZERBO, PO Box 7021, Ouagadougou, 03, Burkina Faso.,Pietro Annigoni Biomolecular Research Center (CERBA), PO Box 364, Ouagadougou, 01, Burkina Faso
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Sadeghpour S, Khodaee S, Rahnama M, Rahimi H, Ebrahimi D. Human APOBEC3 Variations and Viral Infection. Viruses 2021; 13:1366. [PMID: 34372572 PMCID: PMC8310219 DOI: 10.3390/v13071366] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 12/13/2022] Open
Abstract
Human APOBEC3 (apolipoprotein B mRNA-editing catalytic polypeptide-like 3) enzymes are capable of inhibiting a wide range of endogenous and exogenous viruses using deaminase and deaminase-independent mechanisms. These enzymes are essential components of our innate immune system, as evidenced by (a) their strong positive selection and expansion in primates, (b) the evolution of viral counter-defense mechanisms, such as proteasomal degradation mediated by HIV Vif, and (c) hypermutation and inactivation of a large number of integrated HIV-1 proviruses. Numerous APOBEC3 single nucleotide polymorphisms, haplotypes, and splice variants have been identified in humans. Several of these variants have been reported to be associated with differential antiviral immunity. This review focuses on the current knowledge in the field about these natural variations and their roles in infectious diseases.
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Affiliation(s)
- Shiva Sadeghpour
- Department of Biological Science, University of California Irvine, Irvine, CA 92697, USA;
| | - Saeideh Khodaee
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran;
| | - Mostafa Rahnama
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA;
| | - Hamzeh Rahimi
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran;
| | - Diako Ebrahimi
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
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Dias BDC, Paximadis M, Martinson N, Chaisson RE, Ebrahim O, Tiemessen CT. The impact of bone marrow stromal antigen-2 (BST2) gene variants on HIV-1 control in black South African individuals. INFECTION GENETICS AND EVOLUTION 2020; 80:104216. [PMID: 32006707 DOI: 10.1016/j.meegid.2020.104216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/23/2020] [Accepted: 01/28/2020] [Indexed: 12/24/2022]
Abstract
Bone marrow stromal cell antigen 2 (BST2 or tetherin) is a host-encoded, interferon-inducible antiviral restriction factor which blocks the release of enveloped viruses. Few studies have assessed the role of BST2 polymorphisms on HIV-1 acquisition or disease progression in sub-Saharan Africa. This study investigated the frequency of four HIV-1-associated BST2 variants rs3217318, rs12609479, rs10415893 and rs113189798 in uninfected and HIV-1 infected black South Africans. Homozygosity for the rs12609479-A minor allele, previously associated with decreased HIV-1 acquisition risk, was underrepresented in HIV-1 uninfected black South Africans (2%) compared to reference African (9%) and in particular European populations (61%) (p = .047 and p < .0001, respectively). To determine if any of these gene variants influenced HIV-1 control in the absence of antiretroviral treatment (ART), we compared HIV-1 infected ART-naïve progressors [n = 72] and controllers [n = 71], the latter includes elite controllers [EC: n = 23; VL < 50 RNA copies/ml]. Heterozygosity for the rs12609479 SNP (G/A) was enriched in progressors compared to ECs (47.2% vs 21.7%, OR = 3.50 [1.16-10.59], p = .03), while rs113189798 heterozygosity (A/G) showed a strong trend of overrepresentation in ECs compared to progressors (47.8% vs 26.4%, OR = 0.39 [0.14-1.04], p = .07). Heterozygosity for the promoter indel rs3217318 (i19/Δ19) was associated with a faster rate of CD4+ T-cell decline in progressors (p = .0134). Carriage of the rs3217318 (i19/Δ19), rs12609479 (G/G), rs10415893(G/A) and rs113189798 (A/G) combined genotype, denoted as i19Δ19 GG GA AG, was associated with significantly higher CD4+ T-cell counts in progressors (p = .03), a finding predominantly driven by the _GG_AG combination. Our data suggest that the possession of select BST2 genotype combinations may be implicated in HIV-1 disease progression and natural spontaneous control.
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Affiliation(s)
- Bianca Da Costa Dias
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Maria Paximadis
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Neil Martinson
- Perinatal HIV Research Unit (PHRU), SA MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of the Witwatersrand, Johannesburg, South Africa; Centre for TB Research, Johns Hopkins University, Baltimore, USA
| | | | - Osman Ebrahim
- School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Caroline T Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Sorgho PA, Djigma FW, Martinson JJ, Yonli AT, Nagalo BM, Compaore TR, Diarra B, Sombie HK, Simpore A, Zongo AW, Ouattara AK, Soubeiga STR, Traore L, Yelemkoure ET, Kiendrebeogo IT, Roberts LR, Simpore J. Role of Killer cell immunoglobulin-like receptors (KIR) genes in stages of HIV-1 infection among patients from Burkina Faso. Biomol Concepts 2019; 10:226-236. [PMID: 31863692 DOI: 10.1515/bmc-2019-0024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/14/2019] [Indexed: 12/16/2022] Open
Abstract
Objectives A cluster of specialized KIR genes of specialized KIR genes has been shown to be associated with susceptibility or resistance to viral infections in humans. Therefore, this pilot study, this pilot investigation sought to determine the frequencies of KIR genes human immunodeficiency virus type 1( HIV-1) patients and establish their potential clinical involvement in disease progression and staging. Methods HIV-1 infected and healthy individuals were selected for this study. Hepatitis B surface antigen (HBsAg), anti-HCV antibodies and anti-HIV-1/2 antibody/ antigen were screened using a 4th generation ELISA assay (Cobas e 411 Analyzer, Roche Diagnostics GmbH Mannheim, Germany). SSP-PCR was used to evaluate the frequencies of KIR genes. CD4+ T counts and HIV-1 viral load were measured in patients using respectively BD FACSCount and Abbott m2000rt instruments. Results We found a significant association between the frequencies of KIR2DL2 (OR=4.41; p < 0.001), KIR2DS2 (OR=4.76; p < 0.001), KIR2DS3 (OR=2.27; p=0.004), KIR2DS4 (OR=1.76; p=0.026), KIR3DS1 (OR=2.43; p=0.016) and HIV-1 infection; whilst the KIR3DL1 gene (OR= 0.39; p < 0.001) was associated with protection against HIV-1 infection. HIV-1 replication was found to be associated with the presence of KIR2DS2 (OR=6.08, p = 0.024). In contrary the pseudogene KIR2DP1 (OR=0.39; p=0.026) were linked to a protective status with the highest number of lymphocyte T CD4 counts. Conclusion Our data showed that KIR2DL2, KIR2DS2, KIR2DS3, KIR2DS4, and KIR3DS1 were significantly associated with HIV-1 infection whereas KIR3DL1 was associated with protection against HIV-1 infection. Further investigations are needed to fully comprehend the clinical significance of KIR genes in HIV disease progression.
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Affiliation(s)
- Pegdwendé Abel Sorgho
- Laboratory of Molecular Biology and Genetics (LABIOGENE), University Joseph Ki-Zerbo, Ouagadougou, Burkina Faso.,Pietro Annigoni Biomolecular Research Center (CERBA), Ouagadougou, Burkina Faso
| | - Florencia Wendkuuni Djigma
- Laboratory of Molecular Biology and Genetics (LABIOGENE), University Joseph Ki-Zerbo, Ouagadougou, Burkina Faso.,Pietro Annigoni Biomolecular Research Center (CERBA), Ouagadougou, Burkina Faso
| | - Jeremy James Martinson
- Laboratory of Infectious Diseases/ Microbiology, University of Pittsburgh, Pittsburgh, USA
| | - Albert Théophane Yonli
- Laboratory of Molecular Biology and Genetics (LABIOGENE), University Joseph Ki-Zerbo, Ouagadougou, Burkina Faso.,Pietro Annigoni Biomolecular Research Center (CERBA), Ouagadougou, Burkina Faso
| | - Bolni Marius Nagalo
- Division of Hematology & Oncology, Mayo Clinic, Arizona, Scottsdale Arizona, USA
| | - Tégwindé Rebeca Compaore
- Laboratory of Molecular Biology and Genetics (LABIOGENE), University Joseph Ki-Zerbo, Ouagadougou, Burkina Faso.,Institut de Recherche en Sciences de la Sante, IRSS, Ouagadougou, Burkina Faso
| | - Birama Diarra
- Laboratory of Molecular Biology and Genetics (LABIOGENE), University Joseph Ki-Zerbo, Ouagadougou, Burkina Faso
| | - Herman Karim Sombie
- Laboratory of Molecular Biology and Genetics (LABIOGENE), University Joseph Ki-Zerbo, Ouagadougou, Burkina Faso.,Pietro Annigoni Biomolecular Research Center (CERBA), Ouagadougou, Burkina Faso
| | - Abibou Simpore
- Laboratory of Molecular Biology and Genetics (LABIOGENE), University Joseph Ki-Zerbo, Ouagadougou, Burkina Faso
| | - Arsène Wendpagnangdé Zongo
- Laboratory of Molecular Biology and Genetics (LABIOGENE), University Joseph Ki-Zerbo, Ouagadougou, Burkina Faso
| | - Abdoul Karim Ouattara
- Laboratory of Molecular Biology and Genetics (LABIOGENE), University Joseph Ki-Zerbo, Ouagadougou, Burkina Faso
| | - Serge Théophile R Soubeiga
- Laboratory of Molecular Biology and Genetics (LABIOGENE), University Joseph Ki-Zerbo, Ouagadougou, Burkina Faso.,Pietro Annigoni Biomolecular Research Center (CERBA), Ouagadougou, Burkina Faso
| | - Lassina Traore
- Laboratory of Molecular Biology and Genetics (LABIOGENE), University Joseph Ki-Zerbo, Ouagadougou, Burkina Faso
| | - Edwige T Yelemkoure
- Laboratory of Molecular Biology and Genetics (LABIOGENE), University Joseph Ki-Zerbo, Ouagadougou, Burkina Faso.,Pietro Annigoni Biomolecular Research Center (CERBA), Ouagadougou, Burkina Faso
| | - Isabelle Touwendpoulimdé Kiendrebeogo
- Laboratory of Molecular Biology and Genetics (LABIOGENE), University Joseph Ki-Zerbo, Ouagadougou, Burkina Faso.,Pietro Annigoni Biomolecular Research Center (CERBA), Ouagadougou, Burkina Faso
| | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota,USA
| | - Jacques Simpore
- Laboratory of Molecular Biology and Genetics (LABIOGENE), University Joseph Ki-Zerbo, Ouagadougou, Burkina Faso
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Matume ND, Tebit DM, Gray LR, Turner SD, Rekosh D, Bessong PO, Hammarskjöld ML. Characterization of APOBEC3 variation in a population of HIV-1 infected individuals in northern South Africa. BMC MEDICAL GENETICS 2019; 20:21. [PMID: 30660178 PMCID: PMC6339282 DOI: 10.1186/s12881-018-0740-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 12/21/2018] [Indexed: 11/10/2022]
Abstract
BACKGROUND The apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3 (APOBEC3) genes A3D, A3F, A3G and A3H have all been implicated in the restriction of human immunodeficiency virus type 1 (HIV-1) replication. Polymorphisms in these genes are likely to impact viral replication and fitness, contributing to viral diversity. Currently, only a few studies indicate that polymorphisms in the A3 genes may be correlated with infection risk and disease progression. METHODS To characterize polymorphisms in the coding regions of these APOBEC3 genes in an HIV-1 infected population from the Limpopo Province of South Africa, APOBEC3 gene fragments were amplified from genomic DNA of 192 HIV-1 infected subjects and sequenced on an Illumina MiSeq platform. SNPs were confirmed and compared to SNPs in other populations reported in the 1000 Genome Phase III and HapMap databases, as well as in the ExAC exome database. Hardy-Weinberg Equilibrium was calculated and haplotypes were inferred using the LDlink 3.0 web tool. Linkage Disequilibrium (LD) for these SNPS were calculated in the total 1000 genome and AFR populations using the same tool. RESULTS Known variants compared to the GRCh37 consensus genome sequence were detected at relatively high frequencies (> 5%) in all of the APOBEC3 genes. A3H showed the most variation, with several of the variants present in both alleles in almost all of the patients. Several minor allele variants (< 5%) were also detected in A3D, A3F and A3G. In addition, novel R6K, L221R and T238I variants in A3D and I117I in A3F were observed. Four, five, four, and three haplotypes were identified for A3D, A3F, A3G, and A3H respectively. CONCLUSIONS The study showed significant polymorphisms in the APOBEC3D, 3F, 3G and 3H genes in our South African HIV1-infected cohort. In the case of all of these genes, the polymorphisms were generally present at higher frequencies than reported in other 1000 genome populations and in the ExAC exome consortium database .
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Affiliation(s)
- Nontokozo D Matume
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, USA.,HIV/AIDS & Global Health Research Programme and Department of Microbiology, University of Venda, Thohoyandou, South Africa
| | - Denis M Tebit
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, USA.,HIV/AIDS & Global Health Research Programme and Department of Microbiology, University of Venda, Thohoyandou, South Africa.,Global Biomed Scientific LLC, PO Box 2368, Forest, VA, 24551, USA
| | - Laurie R Gray
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, USA
| | - Stephen D Turner
- Department of Public Health Sciences and Bioinformatics Core, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - David Rekosh
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, USA.,HIV/AIDS & Global Health Research Programme and Department of Microbiology, University of Venda, Thohoyandou, South Africa
| | - Pascal O Bessong
- HIV/AIDS & Global Health Research Programme and Department of Microbiology, University of Venda, Thohoyandou, South Africa.
| | - Marie-Louise Hammarskjöld
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, USA. .,HIV/AIDS & Global Health Research Programme and Department of Microbiology, University of Venda, Thohoyandou, South Africa.
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Colón-López DD, Stefan CP, Koehler JW. Emerging viral infections. GENOMIC AND PRECISION MEDICINE 2019. [PMCID: PMC7150306 DOI: 10.1016/b978-0-12-801496-7.00010-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Compaore TR, Soubeiga ST, Ouattara AK, Tchelougou D, Bisseye C, Bakouan DR, Compaore I, Dembele A, Yonli AT, Obiri-Yeboah D, Djigma WF, Simpore J. APOBEC3G expression and HIV-1 infection in Burkina Faso. J Public Health Afr 2018; 9:907. [PMID: 30687488 PMCID: PMC6326155 DOI: 10.4081/jphia.2018.907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 08/14/2018] [Indexed: 11/23/2022] Open
Abstract
APOBEC3G is a potent inhibitor of HIV-1 replication, and act by deaminating cytidines in uracil on the negative strand of the viral cDNA. In this case-control study, APOBEC3G expression in subjects' naïve to HAART infected by HIV-1 and the effect of APOBEC3G polymorphism on its expression were evaluated. The results show that the HIV-1 infected carriers of the G minor alleles of the variant rs8177832 had a higher expression of APOBEC3G mRNA than the controls carriers of the G minor allele. APOBEC3G polymorphisms could play an important role in the modulation of the HIV-1 dissemination.
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Affiliation(s)
- Tegwinde Rebeca Compaore
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Burkina Faso
| | - Serge Theophile Soubeiga
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Burkina Faso
| | - Abdoul Karim Ouattara
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Burkina Faso
| | - Damehan Tchelougou
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Burkina Faso
| | - Cyrille Bisseye
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Burkina Faso
| | - Didier Romuald Bakouan
- Permanent Secretary Against Aids and Sexually Transmitted Diseases, Ouagadougou, Burkina Faso
| | - Issaka Compaore
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Burkina Faso
| | - Augustine Dembele
- Permanent Secretary Against Aids and Sexually Transmitted Diseases, Ouagadougou, Burkina Faso
| | - Albert Theophane Yonli
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Burkina Faso
| | - Dorcas Obiri-Yeboah
- Microbiology Department, School of Medical Sciences, University of Cape Coast, Ghana
| | | | - Jacques Simpore
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Burkina Faso
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Insights into the Interplay between KIR Gene Frequencies and Chronic HBV Infection in Burkina Faso. Mediterr J Hematol Infect Dis 2018; 10:e2018060. [PMID: 30416692 PMCID: PMC6223576 DOI: 10.4084/mjhid.2018.060] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 10/01/2018] [Indexed: 12/13/2022] Open
Abstract
Background/Objective Hepatitis B virus (HBV) infection is the leading risk factor for cirrhosis and hepatocellular carcinoma (HCC). The objective of this investigation was to assess the association between “Killer Cell Immunoglobulin-Like Receptor” (KIR) gene frequencies and chronic HBV infection. Methods Chronic HBV carriers and healthy patients were selected for this study. The viral load for HBV were performed, and SSP-PCR was used to characterize the frequencies of KIR genes. Results The study suggested that inhibitory genes KIR2DL2 (crude OR = 2.82; p < 0.001), KIR2DL3 (crude OR = 2.49; p < 0.001) and activator gene KIR2DS2 (crude OR = 3.95; p< 0.001) might be associated with chronic stages of HBV infection. Conversely the inhibitory genes KIR3DL1 (crude OR = 0.49; p = 0.0018) and KIR3DL2 (crude OR = 0.41; p = 0.005), the activator gene KIR2DS1 (crude OR = 0.48; p = 0.014) and the pseudo gene KIR2DP1 (crude OR = 0.49; p = 0.008) could be associated with immunity against HBV infection. Chronic HBV patients who are carriers for the KIR3DL3 gene (crude OR = 8; p = 0.048) were positive for HBeAg and patients who carried the KIR3DL2 gene (crude OR = 3.21; p = 0.012) had a high HBV viral load compared to the rest of the study population. Conclusion Our data showed evidence of a correlation between the risk of developing chronic HBV infection and certain KIR gene frequencies and also show that KIR3DL1, KIR3DL2, KIR2DS1 might confer a protective status against chronic HBV infection.
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Scagnolari C, Antonelli G. Type I interferon and HIV: Subtle balance between antiviral activity, immunopathogenesis and the microbiome. Cytokine Growth Factor Rev 2018; 40:19-31. [PMID: 29576284 PMCID: PMC7108411 DOI: 10.1016/j.cytogfr.2018.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 02/23/2018] [Accepted: 03/08/2018] [Indexed: 02/06/2023]
Abstract
Induction and action of IFN during acute and chronic HIV-1 infection. Host and viral factors influencing IFN response in HIV-1 infected patients. Type I IFN and IFNα subtypes signatures and their antiviral activity during HIV-1 infection. The microbiome and intestinal IFN responses relationship in HIV-1 infection and disease.
Type I interferon (IFN) response initially limits HIV-1 spread and may delay disease progression by stimulating several immune system components. Nonetheless, persistent exposure to type I IFN in the chronic phase of HIV-1 infection is associated with desensitization and/or detrimental immune activation, thereby hindering immune recovery and fostering viral persistence. This review provides a basis for understanding the complexity and function of IFN pleiotropic activity in HIV-1 infection. In particular, the dichotomous role of the IFN response in HIV-1 immunopathogenesis will be discussed, highlighting recent advances in the dynamic modulation of IFN production in acute versus chronic infection, expression signatures of IFN subtypes, and viral and host factors affecting the magnitude of IFN response during HIV-1 infection. Lastly, the review gives a forward-looking perspective on the interplay between microbiome compositions and IFN response.
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Affiliation(s)
- Carolina Scagnolari
- Department of Molecular Medicine, Laboratory of Virology Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy.
| | - Guido Antonelli
- Department of Molecular Medicine, Laboratory of Virology Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy
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11
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Iqbal K, Imran M, Ullah S, Jamal M, Waheed Y, Ali Q. Correlation of Apolipoprotein B mRNA-editing Enzyme, Catalytic Polypeptide- like 3G Genetic Variant rs8177832 with HIV-1 Predisposition in Pakistani Population. Curr HIV Res 2018; 16:297-301. [PMID: 30338740 PMCID: PMC6416456 DOI: 10.2174/1570162x16666181018155827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 10/08/2018] [Accepted: 10/12/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND Human immunodeficiency virus (HIV) infection is a global health burden which ultimately results in acquired immune deficiency syndrome (AIDS). There are multiple host factors which are capable of limiting HIV-1 replication. One of the most important host factors which inhibit HIV-1 DNA synthesis is the apolipoprotein B mRNA-editing enzyme, catalytic polypeptide- like 3G (APOBEC3G). Any genetic variation of this important host factor may influence the host susceptibility to viral infection. OBJECTIVE The aim of the current study was to evaluate any correlation of APOBEC3G genetic variation rs8177832 with HIV-1 infection. METHODS The study involved 142 healthy control and 100 HIV-1 infected subjects. The genetic variation rs8177832 of all studied subjects was determined by allele-specific polymerase chain reaction (AS-PCR). RESULTS The results showed that the distribution of rs8177832 genotypes AA, AG and GG in healthy subjects and HIV-1 subjects was; 42.253%, 42.957%, 14.788% and 66%, 27%, 7% respectively. Statistical analyses of data showed that there was a significant variation in rs8177832 genotype AA in healthy control and HIV-1 infected subjects (42.257% vs 66%; p-value<0.001). CONCLUSION Thus it was concluded that APOBEC3G rs8177832 AA genotype contributes in genetic predisposition to HIV-1 infection in Pakistani population.
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Affiliation(s)
- Khurshid Iqbal
- Address correspondence to this author at the Department of Medical Laboratory Sciences, Imperial College of Business Studies, Lahore, Pakistan; Tel: 00923028051657; E-mail:
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12
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Genetic and immune determinants of immune activation in HIV-exposed seronegative individuals and their role in protection against HIV infection. INFECTION GENETICS AND EVOLUTION 2017; 66:325-334. [PMID: 29258786 DOI: 10.1016/j.meegid.2017.12.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 12/12/2017] [Accepted: 12/14/2017] [Indexed: 12/13/2022]
Abstract
Soon thereafter infection is established, hosts strive for an efficient eradication of microorganisms, with as limited tissue damage as possible, and durable immunological protection against re-infection. On the other hand, pathogens have developed countermeasures to escape host surveillance and to warrant diffusion to other hosts. In this molecular arms race the final results relies on multiple variables, including the genetic and immunologic e correlates of protection available for the host. In the field of HIV-infection, natural protection has been repeatedly associated to the presence of an immune activation state, at least in some cohorts of HESN (HIV-exposed seronegative). Indeed, these subjects, who naturally resist HIV-infection despite repeated exposure to the virus, are characterized by an increased expression of activation markers on circulating cells and greater production of immunological effector molecules both in basal condition and upon specific-stimulation. Although these results are not univocally shared, several publications emphasize the existence of a correlation between polymorphisms in genes associated with increased immune activation and the HESN phenotype. In this review, we will describe some of the genetic variants associated with protection against HIV infection. Understanding the basis of HIV resistance in HESN is mandatory to develop new preventative and therapeutic interventions.
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Li Q, Qiao Y, Zhang G, He N, Zhang X, Jia X, Sun H, Wang C, Xu L. Association of single nucleotide polymorphisms of APOBEC3G with susceptibility to HIV-1 infection and disease progression among men engaging in homosexual activity in northern China. Arch Virol 2016; 162:259-268. [PMID: 27730383 DOI: 10.1007/s00705-016-3080-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 09/19/2016] [Indexed: 11/27/2022]
Abstract
Men who have sex with men (MSM) are at high risk of HIV infection. The APOBEC3G (apolipoprotein B mRNA editing catalytic polypeptide 3G) protein is a component of innate antiviral immunity that inhibits HIV-1 replication. In the present study, a total of 483 HIV-1 seropositive men and 493 HIV-1 seronegative men were selected to investigate the association between single nucleotide polymorphisms (SNPs) of the APOBEC3G gene and susceptibility to HIV-1 infection and AIDS progression among MSM residing in northern China. Genotyping of four SNPs (rs5757465, rs3736685, rs8177832, and rs2899313) of the APOBEC3G was performed using the SNPscan™ Kit, while the rs2294367 polymorphism was genotyped using the SNaPshot multiplex system. Our results disclosed no association between the SNPs of APOBEC3G and susceptibility to HIV-1, or effects of these polymorphisms on the CD4+ T cell count or clinical phase of disease. A meta-analysis of 1624 men with HIV-1 infection and 1523 controls suggested that the association between rs8177832 and susceptibility was not significant. However, we observed a trend towards association with HIV-1 infection for haplotype TTACA (p = 0.082). The potential role of variants of APOBEC3G in HIV-1/AIDS warrants further investigation.
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Affiliation(s)
- Qiuyan Li
- Laboratory of Medical Genetics, Harbin Medical University, Baojian Road 157, Nangang District, Harbin, 150081, People's Republic of China
| | - Yuandong Qiao
- Laboratory of Medical Genetics, Harbin Medical University, Baojian Road 157, Nangang District, Harbin, 150081, People's Republic of China
| | - Guangfa Zhang
- Laboratory of Medical Genetics, Harbin Medical University, Baojian Road 157, Nangang District, Harbin, 150081, People's Republic of China
| | - Ning He
- Department of Clinical Laboratory, Qiqihar Traditional Chinese Medicine Hospital, Qiqihar, 161000, People's Republic of China
| | - Xuelong Zhang
- Laboratory of Medical Genetics, Harbin Medical University, Baojian Road 157, Nangang District, Harbin, 150081, People's Republic of China
| | - Xueyuan Jia
- Laboratory of Medical Genetics, Harbin Medical University, Baojian Road 157, Nangang District, Harbin, 150081, People's Republic of China
| | - Haiming Sun
- Laboratory of Medical Genetics, Harbin Medical University, Baojian Road 157, Nangang District, Harbin, 150081, People's Republic of China
| | - Chuntao Wang
- Laboratory of Medical Genetics, Harbin Medical University, Baojian Road 157, Nangang District, Harbin, 150081, People's Republic of China
| | - Lidan Xu
- Laboratory of Medical Genetics, Harbin Medical University, Baojian Road 157, Nangang District, Harbin, 150081, People's Republic of China.
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Compaore TR, Diarra B, Assih M, Obiri-Yeboah D, Soubeiga ST, Ouattara AK, Tchelougou D, Bisseye C, Bakouan DR, Compaore IP, Dembele A, Djigma WF, Simpore J. HBV/HIV co-infection and APOBEC3G polymorphisms in a population from Burkina Faso. BMC Infect Dis 2016; 16:336. [PMID: 27449138 PMCID: PMC4957463 DOI: 10.1186/s12879-016-1672-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 06/16/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3G (APOBEC3G) is a potent host defense factor, which interferes with HIV-1 and HBV. Our study had three objectives, to screen a population of HIV-1 infected and uninfected patients in Burkina Faso for HBV, to screen the population for APOBEC3G variants rs6001417, rs8177832, and rs35228531 previously described, and to analyze the effect of these three variants and their haplotypes on HIV-1/HBV co-infection in Burkina Faso. METHODS HBV detection was performed on samples from HIV-1 infected and uninfected subjects using rapid detection tests and real-time PCR. APOBEC3 genotyping was done by the TaqMan allelic discrimination method. Fisher Exact test, Odds ratio (OR), confidence intervals (CI) at 95 %, Linkage disequilibrium (LD) summary statistics and haplotype frequencies were calculated. RESULTS The prevalence of HBV was 56.7 % among HIV-1 positive patients of our study while it was about 12.8 % among HIV-1 seronegative subjects. Genotype E was the genotype of HBV present in our hepatitis B positive samples. Minor allele frequencies of rs6001417, rs8177832, and rs35228531 were higher in seronegative subjects. The T minor allele of variant rs35228531 was protective against HIV-1/HBV co-infection with OR = 0.61, 95 % CI (0.42-0.90), p = 0.013. There was also an association between the GGT haplotype and protection against HIV-1/HBV co-infection, OR = 0.57, 95 % CI (0.33-0.99), p = 0.050. The other haplotypes present in the population were not statistically significant. There minor allele T of the rs35228531 was protective against HIV mono-infection OR = 0.53, 95 % CI (0.3-0.93), P = 0.030. But there was no effect of protection against HBV mono-infection. CONCLUSION APOBEC3G through its variants rs6001417, rs8177832, and rs35228531, in this study interferes with HIV-1/HBV co-infection could be due the HIV-1 mono-infection in a population from Burkina Faso.
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Affiliation(s)
- Tegwinde Rebeca Compaore
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Birama Diarra
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Maleki Assih
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Dorcas Obiri-Yeboah
- Department of Microbiology and Immunology, School of Medical Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Serge Theophile Soubeiga
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Abdoul Karim Ouattara
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Damehan Tchelougou
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Cyrille Bisseye
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Didier Romuald Bakouan
- Permanent Secretary against Aids and sexually transmitted diseases, Ouagadougou, Burkina Faso
| | - Issaka Pierre Compaore
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Augustine Dembele
- Permanent Secretary against Aids and sexually transmitted diseases, Ouagadougou, Burkina Faso
| | - Wendkuuni Florencia Djigma
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Jacques Simpore
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso.
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