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Laplana M, Royo JL, Real LM. Genetic Association Studies in Host-Pathogen Interaction Analysis. Methods Mol Biol 2024; 2751:19-30. [PMID: 38265707 DOI: 10.1007/978-1-0716-3617-6_2] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Studying host-pathogen interactions at a molecular level has always been technically challenging. Identifying the different biochemical and genetic pathways involved in the different stages of infection traditionally require complex molecular biology tools and often the use of costly animal models. In this chapter, we illustrate a complementary approach to address host-pathogen interactions, taking advantage of the natural interindividual genetic diversity. The application of genetic association studies allows us to identify alleles involved in infection progression or resistance. Thus, this strategy may be useful to unravel new molecular pathways underlying host-pathogen interactions. Here we present the general steps that might be followed to plan, execute, and analyze a population-based study in order to identify genetic variants affecting human exposition to pathogens.
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Affiliation(s)
- Marina Laplana
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - José Luis Royo
- Departamento de Especialidades Quirúrgicas, Bioquímica e Inmunología. Facultad de Medicina, Universidad de Málaga, Málaga, Spain.
| | - Luis Miguel Real
- Departamento de Especialidades Quirúrgicas, Bioquímica e Inmunología. Facultad de Medicina, Universidad de Málaga, Málaga, Spain
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario de Valme, Sevilla, Spain
- Centro de Investigación en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
- Instituto de Biomedicina de Sevilla, Sevilla, Spain
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Gluchowski M, Yu X, Abrenica B, Yao S, Kimani J, Douville RN, Ball TB, Su R. Transient Increases in Inflammation and Proapoptotic Potential Are Associated with the HESN Phenotype Observed in a Subgroup of Kenyan Female Sex Workers. Viruses 2022; 14:471. [PMID: 35336878 PMCID: PMC8948937 DOI: 10.3390/v14030471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/13/2022] [Accepted: 02/21/2022] [Indexed: 01/27/2023] Open
Abstract
Interferon (IFN) -stimulated genes (ISGs) are critical effectors of IFN response to viral infection, but whether ISG expression is a correlate of protection against HIV infection remains elusive. A well-characterized subcohort of Kenyan female sex workers, who, despite being repeatedly exposed to HIV-1 remain seronegative (HESN), exhibit reduced baseline systemic and mucosal immune activation. This study tested the hypothesis that regulation of ISGs in the cells of HESN potentiates a robust antiviral response against HIV. Transcriptional profile of a panel of ISGs with antiviral function in PBMC and isolated CD4+ T cells from HESN and non-HESN sex worker controls were defined following exogenous IFN-stimulation using relative RT-qPCR. This study identified a unique profile of proinflammatory and proapoptotic ISGs with robust but transient responses to exogenous IFN-γ and IFN-α2 in HESN cells. In contrast, the non-HESN cells had a strong and prolonged proinflammatory ISG profile at baseline and following IFN challenge. Potential mechanisms may include augmented bystander apoptosis due to increased TRAIL expression (16-fold), in non-HESN cells. The study also identified two negative regulators of ISG induction associated with the HESN phenotype. Robust upregulation of SOCS-1 and IRF-1, in addition to HDM2, could contribute to the strict regulation of proinflammatory and proapoptotic ISGs in HESN cells. As reducing IRF-1 in the non-HESN cells resulted in the identified HESN ISG profile, and decreased HIV susceptibility, the unique HESN ISG profile could be a correlate of protection against HIV infection.
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Serrano-Rísquez C, Omar M, Gómez-Vidal MA, Real LM, Pineda JA, Rivero A, Rivero-Juárez A, Forthal D, Márquez FJ, Lo Caputo S, Clerici M, Biasin M, Caruz A. CD46 Genetic Variability and HIV-1 Infection Susceptibility. Cells 2021; 10:3094. [PMID: 34831317 DOI: 10.3390/cells10113094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/04/2021] [Indexed: 02/07/2023] Open
Abstract
CD46 is the main receptor for complement protein C3 and plays an important role in adaptive immune responses. CD46 genetic variants are associated with susceptibility to several infectious and autoimmune diseases. Additionally, CD46 function can be subverted by HIV-1 to evade attack by complement, a strategy shared by viruses of other families. We sought to determine the association between CD46 gene variants and HIV-1 acquired through intravenous drug use (IDU) and sexual routes (n = 823). Study subjects were of European ancestry and were HIV-1 infected (n = 438) or exposed but seronegative (n = 387). Genotyping of the rs2796265 SNP located in the CD46 gene region was done by allele-specific real-time PCR. A meta-analysis merging IDU and sexual cohorts indicates that the minor genotype (CC) was associated with increased resistance to HIV-1 infection OR = 0.2, 95% CI (0.07–0.61), p = 0.004. The HIV-1-protective genotype is correlated with reduced CD46 expression and alterations in the ratio of CD46 mRNA splicing isoforms.
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Vastrad B, Vastrad C, Tengli A. Bioinformatics analyses of significant genes, related pathways, and candidate diagnostic biomarkers and molecular targets in SARS-CoV-2/COVID-19. Gene Rep 2020; 21:100956. [PMID: 33553808 DOI: 10.1016/j.genrep.2020.100956] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/31/2020] [Indexed: 12/12/2022]
Abstract
Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) infection is a leading cause of pneumonia and death. The aim of this investigation is to identify the key genes in SARS-CoV-2 infection and uncover their potential functions. We downloaded the expression profiling by high throughput sequencing of GSE152075 from the Gene Expression Omnibus database. Normalization of the data from primary SARS-CoV-2 infected samples and negative control samples in the database was conducted using R software. Then, joint analysis of the data was performed. Pathway and Gene ontology (GO) enrichment analyses were performed, and the protein-protein interaction (PPI) network, target gene - miRNA regulatory network, target gene - TF regulatory network of the differentially expressed genes (DEGs) were constructed using Cytoscape software. Identification of diagnostic biomarkers was conducted using receiver operating characteristic (ROC) curve analysis. 994 DEGs (496 up regulated and 498 down regulated genes) were identified. Pathway and GO enrichment analysis showed up and down regulated genes mainly enriched in the NOD-like receptor signaling pathway, Ribosome, response to external biotic stimulus and viral transcription in SARS-CoV-2 infection. Down and up regulated genes were selected to establish the PPI network, modules, target gene - miRNA regulatory network, target gene - TF regulatory network revealed that these genes were involved in adaptive immune system, fluid shear stress and atherosclerosis, influenza A and protein processing in endoplasmic reticulum. In total, ten genes (CBL, ISG15, NEDD4, PML, REL, CTNNB1, ERBB2, JUN, RPS8 and STUB1) were identified as good diagnostic biomarkers. In conclusion, the identified DEGs, hub genes and target genes contribute to the understanding of the molecular mechanisms underlying the advancement of SARS-CoV-2 infection and they may be used as diagnostic and molecular targets for the treatment of patients with SARS-CoV-2 infection in the future.
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Key Words
- Bioinformatics
- CBL, Cbl proto-oncogene
- DEGs, differentially expressed genes
- Diagnosis
- GO, Gene ontology
- ISG15, ISG15 ubiquitin like modifier
- Key genes
- NEDD4, NEDD4 E3 ubiquitin protein ligase
- PML, promyelocyticleukemia
- PPI, protein-protein interaction
- Pathways
- REL, REL proto-oncogene, NF-kB subunit
- ROC, receiver operating characteristic
- SARS-CoV-2 infection
- SARS-CoV-2, Severe acute respiratory syndrome corona virus 2
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Chen H, Moussa M, Catalfamo M. The Role of Immunomodulatory Receptors in the Pathogenesis of HIV Infection: A Therapeutic Opportunity for HIV Cure? Front Immunol 2020; 11:1223. [PMID: 32714317 PMCID: PMC7343933 DOI: 10.3389/fimmu.2020.01223] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 05/15/2020] [Indexed: 12/12/2022] Open
Abstract
Immune activation is the hallmark of HIV infection and plays a role in the pathogenesis of the disease. In the context of suppressed HIV RNA replication by combination antiretroviral therapy (cART), there remains immune activation which is associated to the HIV reservoirs. Persistent virus contributes to a sustained inflammatory environment promoting accumulation of "activated/exhausted" T cells with diminished effector function. These T cells show increased expression of immunomodulatory receptors including Programmed cell death protein (PD1), Cytotoxic T Lymphocyte Associated Protein 4 (CTLA4), Lymphocyte activation gene 3 (LAG3), T cell immunoglobulin and ITIM domain (TIGIT), T cell immunoglobulin and mucin domain containing 3 (TIM3) among others. More importantly, recent reports had demonstrated that, HIV infected T cells express checkpoint receptors, contributing to their survival and promoting maintenance of the viral reservoir. Therapeutic strategies are focused on viral reservoir elimination and/or those to achieve sustained cART-free virologic remission. In this review, we will discuss the immunological basis and the latest advances of the use of checkpoint inhibitors to treat HIV infection.
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Affiliation(s)
- Hui Chen
- Department of Microbiology and Immunology, Georgetown University School of Medicine, Washington, DC, United States
- CMRS/Laboratory of Immunoregulation, National Institutes of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Maha Moussa
- Department of Microbiology and Immunology, Georgetown University School of Medicine, Washington, DC, United States
| | - Marta Catalfamo
- Department of Microbiology and Immunology, Georgetown University School of Medicine, Washington, DC, United States
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Fenizia C, Saulle I, Clerici M, Biasin M. Genetic and epigenetic regulation of natural resistance to HIV-1 infection: new approaches to unveil the HESN secret. Expert Rev Clin Immunol 2020; 16:429-445. [PMID: 32085689 DOI: 10.1080/1744666x.2020.1732820] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Introduction: Since the identification of HIV, several studies reported the unusual case of small groups of subjects showing natural resistance to HIV infection. These subjects are referred to as HIV-1-exposed seronegative (HESN) individuals and include people located in different areas, with diverse ethnic backgrounds and routes of exposure. The mechanism/s responsible for protection from infection in HESN individuals are basically indefinite and most likely are multifactorial.Areas covered: Host factors, including genetic background as well as natural and acquired immunity, have all been associated with this phenomenon. Recently, epigenetic factors have been investigated as possible determinants of reduced susceptibility to HIV infection. With the advent of the OMICS era, the availability of techniques such as GWAS, RNAseq, and exome-sequencing in both bulk cell populations and single cells will likely lead to great strides in the understanding of the HESN mystery.Expert opinion: The employment of increasingly sophisticated techniques is allowing the gathering of enormous amounts of data. The integration of such information will provide important hints that could lead to the identification of viral and host correlates of protection against HIV infection, allowing the development of more effective preventative and therapeutic regimens.
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Affiliation(s)
- Claudio Fenizia
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy
| | - Irma Saulle
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy.,Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Mara Biasin
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan, Italy
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Jaimes-Bernal C, Rallón N, Benito JM, Omar M, Gómez-Vidal MA, Márquez FJ, Sánchez-Arcas B, Trujillo M, Royo JL, Saulle I, Biasin M, Rivero-Juárez A, Caruz A. A Knockout IFNL4 Variant Is Associated With Protection From Sexually Transmitted HIV-1 Infection. J Infect Dis 2019; 219:772-776. [PMID: 30289470 DOI: 10.1093/infdis/jiy584] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 10/04/2018] [Indexed: 11/14/2022] Open
Abstract
An interferon λ4 gene (IFNL4) knockout allele (rs368234815; TT) is associated with spontaneous and IFN-α-dependent cure of hepatitis C virus infection. The role of this polymorphism in the susceptibility to human immunodeficiency virus type 1 (HIV-1) infection is controversial. This study aimed to assess the association of this knockout IFNL4 variant and sexually transmitted HIV-1 infection. A total of 228 HIV-1-positive individuals and 136 HIV-exposed seronegative individuals were investigated for their association with IFNL4 rs368234815 genotypes. The IFNL4 ΔG functional allele is associated with increased susceptibility to HIV-1 infection through the sexual route (odds ratio [OR], 2.1; 95% confidence interval [CI], 1.2-3.6; P = .004). A meta-analysis including a population of injection drug users suggests a codominant mode of inheritance of this risk factor (OR, 2.0; 95% CI, 1.3-3.2; P = .001).
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Affiliation(s)
- Claudia Jaimes-Bernal
- Immunogenetics Unit, Department of Experimental Biology, Universidad de Jaén, Jaen.,Research Group of the Bacteriology and Clinical Laboratory Program, Faculty of Health Sciences, Universidad de Boyacá, Tunja, Colombia
| | - Norma Rallón
- Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Madrid.,Hospital Universitario Rey Juan Carlos, Móstoles
| | - José M Benito
- Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Madrid.,Hospital Universitario Rey Juan Carlos, Móstoles
| | - Mohamed Omar
- Infectious Diseases and Clinical Microbiology Unit. Complejo Hospitalario de Jaén, Jaen
| | | | | | | | | | - José Luis Royo
- Department of Surgery, Biochemistry and Immunology, Universidad de Málaga, Málaga
| | - Irma Saulle
- Department of Biomedical and Clinical Sciences "L.-Sacco", University of Milan, Italy
| | - Mara Biasin
- Department of Biomedical and Clinical Sciences "L.-Sacco", University of Milan, Italy
| | - Antonio Rivero-Juárez
- Maimonides Institute for Research in Biomedicine of Cordoba/Hospital Universitario Reina Sofía, Cordoba, Spain
| | - Antonio Caruz
- Immunogenetics Unit, Department of Experimental Biology, Universidad de Jaén, Jaen
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Fenizia C, Rossignol JF, Clerici M, Biasin M. Genetic and immune determinants of immune activation in HIV-exposed seronegative individuals and their role in protection against HIV infection. Infect Genet Evol 2018; 66:325-34. [PMID: 29258786 DOI: 10.1016/j.meegid.2017.12.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [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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Su RC, Plesniarski A, Ao Z, Kimani J, Sivro A, Jaoko W, Plummer FA, Yao X, Ball TB. Reducing IRF-1 to Levels Observed in HESN Subjects Limits HIV Replication, But Not the Extent of Host Immune Activation. Mol Ther Nucleic Acids 2015; 4:e259. [PMID: 26506037 DOI: 10.1038/mtna.2015.29] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/19/2015] [Indexed: 12/14/2022]
Abstract
Cells from women who are epidemiologically deemed resistant to HIV infection exhibit a 40-60% reduction in endogenous IRF-1 (interferon regulatory factor-1), an essential regulator of host antiviral immunity and the early HIV replication. This study examined the functional consequences of reducing endogenous IRF-1 on HIV-1 replication and immune response to HIV in natural HIV target cells. IRF-1 knockdown was achieved in ex vivo CD4(+) T cells and monocytes with siRNA. IRF-1 level was assessed using flow cytometry, prior to infection with HIV-Bal, HIV-IIIB, or HIV-VSV-G. Transactivation of HIV long terminal repeats was assessed by p24 secretion (ELISA) and Gag expression (reverse transcription-polymerase chain reaction (RT-PCR)). The expression of IRF-1-regulated antiviral genes was quantitated with RT-PCR. A modest 20-40% reduction in endogenous IRF-1 was achieved in >87% of ex vivo-derived peripheral CD4(+) T cells and monocytes, resulted in >90% reduction in the transactivation of the HIV-1 genes (Gag, p24) and, hence, HIV replication. Curiously, these HIV-resistant women demonstrated normal immune responses, nor an increased susceptibility to other infection. Similarly, modest IRF-1 knockdown had limited impact on the magnitude of HIV-1-elicited activation of IRF-1-regulated host immunologic genes but resulted in lessened duration of these responses. These data suggest that early expression of HIV-1 genes requires a higher IRF-1 level, compared to the host antiviral genes. Together, these provide one key mechanism underlying the natural resistance against HIV infection and further suggest that modest IRF-1 reduction could effectively limit productive HIV infection yet remain sufficient to activate a robust but transient immune response.
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Abstract
PURPOSE OF REVIEW Rapid expansion of genomic technologies has resulted in an unprecedented ability to interrogate the impact of human genetic variation on disease. HIV-1 infection is a unique model for studying this impact because host genetic variation influences both clinical outcome and the genetic sequence and evolution of the pathogen itself. RECENT FINDINGS Several candidate gene studies have proposed novel associations with HIV acquisition and/or disease progression; however, many of these are not supported by larger genome-wide association studies. Thus, controversy remains as to which host and viral genetic factors truly impact HIV infection. Novel methods for assessing the genetic (viral and host) component of disease progression are becoming important areas of investigation. SUMMARY To fully understand the impact of human genetic variation in HIV disease, the field will need to come together to set a standard for discovery of new genes. Additionally, novel avenues of investigation such as sequencing studies (to define the role of rare variants), studies of epistasis and host/viral genome interaction will be of great value.
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Taborda NA, Hernández JC, Lajoie J, Juno JA, Kimani J, Rugeles MT, Fowke KR. Short Communication: Low Expression of Activation and Inhibitory Molecules on NK Cells and CD4(+) T Cells Is Associated with Viral Control. AIDS Res Hum Retroviruses 2015; 31:636-40. [PMID: 25738606 DOI: 10.1089/aid.2014.0325] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chronic HIV-1 infection induces severe immune alterations, including hyperactivation, exhaustion, and apoptosis. In fact, viral control has been associated with low frequencies of these processes. Here, we evaluated the expression of activation and inhibitory molecules on natural killer (NK) and CD4(+) T cells and plasma levels of proinflammatory cytokines in individuals exhibiting viral control: a cohort of HIV-1-exposed-seronegative individuals (HESN) and a cohort of HIV controllers. There was lower expression of CD69, LAG-3, PD-1, and TIM-3 in both cohorts when compared to a low-risk population or HIV progressors. In addition, HIV controllers exhibited lower plasma levels of proinflamatory molecules TNF-α and IP-10. These findings suggest that individuals exhibiting viral control have lower basal expression of markers associated with cellular activation and particularly immune exhaustion.
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Affiliation(s)
- Natalia A. Taborda
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Juan C. Hernández
- Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín, Colombia
| | - Julie Lajoie
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jennifer A. Juno
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Joshua Kimani
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - María T. Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Keith R. Fowke
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
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