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Esman A, Salamaikina S, Kirichenko A, Vinokurov M, Fomina D, Sikamov K, Syrkina A, Pokrovskaya A, Akimkin V. Promoter Methylation of HIV Coreceptor-Related Genes CCR5 and CXCR4: Original Research. Viruses 2025; 17:465. [PMID: 40284908 PMCID: PMC12030890 DOI: 10.3390/v17040465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2025] [Revised: 03/03/2025] [Accepted: 03/06/2025] [Indexed: 04/29/2025] Open
Abstract
The persistence of human immunodeficiency virus (HIV) within viral reservoirs poses significant challenges to eradication efforts. Epigenetic alterations, including DNA methylation, are potential factors influencing the latency and persistence of HIV. This study details the development and application of techniques to assess CpG methylation in the promoter regions of the CCR5 and CXCR4 genes, which are key HIV-1 coreceptors. Using both Sanger sequencing and pyrosequencing methods, we examined 51 biological samples from 17 people living with HIV at three time points: baseline (week 0) and post-antiretroviral therapy (ART) at weeks 24 and 48. Our results revealed that CXCR4 promoter CpG sites were largely unmethylated, while CCR5 promoter CpGs exhibited significant variability in methylation levels. Specifically, CCR5 CpG 1 showed a significant decrease in methylation from week 0 to week 48, while CXCR4 CpG 3 displayed a significant decrease between week 0 and week 24. These differences were statistically significant when compared with non-HIV-infected controls. These findings demonstrate distinct methylation patterns between CCR5 and CXCR4 promoters in people living with HIV over time, suggesting that epigenetic modifications may play a role in regulating the persistence of HIV-1. Our techniques provide a reliable framework for assessing gene promoter methylation and could be applied in further research on the epigenetics of HIV.
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Affiliation(s)
- Anna Esman
- Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Central Research Institute of Epidemiology, 111123 Moscow, Russia
| | - Svetlana Salamaikina
- Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Central Research Institute of Epidemiology, 111123 Moscow, Russia
| | - Alina Kirichenko
- Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Central Research Institute of Epidemiology, 111123 Moscow, Russia
| | - Michael Vinokurov
- Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Central Research Institute of Epidemiology, 111123 Moscow, Russia
| | - Darya Fomina
- Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Central Research Institute of Epidemiology, 111123 Moscow, Russia
- State Research Center—Burnazyan Federal Medical Biophysical Center of Federal Medical Biological Agency, 123098 Moscow, Russia
| | - Kirill Sikamov
- Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Central Research Institute of Epidemiology, 111123 Moscow, Russia
| | - Arina Syrkina
- Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Central Research Institute of Epidemiology, 111123 Moscow, Russia
| | - Anastasia Pokrovskaya
- Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Central Research Institute of Epidemiology, 111123 Moscow, Russia
- Medical Institute, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Vasily Akimkin
- Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Central Research Institute of Epidemiology, 111123 Moscow, Russia
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Baroncini L, Muller CKS, Kadzioch NP, Wolfensberger R, Russenberger D, Bredl S, Mlambo T, Speck RF. Pro-inflammatory macrophages suppress HIV replication in humanized mice and ex vivo co-cultures. Front Immunol 2024; 15:1439328. [PMID: 39575258 PMCID: PMC11578737 DOI: 10.3389/fimmu.2024.1439328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 10/04/2024] [Indexed: 11/24/2024] Open
Abstract
Introduction Very little is known about the role of macrophages as immune mediators during natural HIV infection. Humanized mice are an extremely valuable in vivo model for studying HIV pathogenesis. However, the presence of murine mononuclear phagocytes in these models represents a significant limitation for studying their human counterpart. Therefore, we have developed a novel humanized mouse model that allows selective depletion of human myeloid cells at a time point of our choosing. Methods We genetically engineered human hematopoietic stem and progenitor cells (HSPCs) to express an inducible caspase-9 (iCas9) suicide system under a synthetic myeloid promoter. Using these HSPCs, we generated humanized mice. iCasp9 induction in vivo resulted in selective human myeloid cell death in this inducible human myeloid depletion (iHMD) mouse model. In addition, we co-cultured monocyte-derived macrophages with ex vivo HIV-infected PBMCs to further mechanistically investigate the effect of macrophages on HIV replication using flow cytometry, cytokine analysis, and RNA sequencing of both macrophages and CD4+ T cells. Results HIV infection induced a pro-inflammatory phenotype in HIV-infected humanized NSG mice during the early and late stages of HIV infection. Myeloid cell depletion in HIV-infected iHMD-NSG mice resulted in a rapid increase in HIV RNA replication, which was accompanied by a loss of pro-inflammatory cytokines. Co-culture of macrophages with ex vivo HIV-infected PBMCs reproduced their anti-HIV effects observed in vivo. Transcriptomic data showed macrophages upregulate antiviral cytokines and chemokines in co-culture, while inducing CD4+ T cells to upregulate HIV restriction factors and downregulate pathways involved in protein expression and cell replication. Discussion This study describes a novel role of macrophages as effector cells, both ex vivo and in vivo, acting against HIV replication and limiting disease progression.
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Affiliation(s)
| | | | | | | | | | | | | | - Roberto F. Speck
- Department of Infectious Diseases and Hospital Epidemiology, University of Zurich,
University Hospital of Zurich, Zurich, Switzerland
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Coleman SL, Neff CP, Li SX, Armstrong AJ, Schneider JM, Sen S, Fennimore B, Campbell TB, Lozupone CA, Palmer BE. Can gut microbiota of men who have sex with men influence HIV transmission? Gut Microbes 2020; 11:610-619. [PMID: 32036739 PMCID: PMC7524317 DOI: 10.1080/19490976.2019.1700756] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Gaining a complete understanding of transmission risk factors will assist in efforts to reduce new HIV infections, especially within the disproportionally affected population of men who have sex with men (MSM). We recently reported that the fecal microbiota of MSM elevates immune activation in gnotobiotic mice and enhances HIV infection in vitro over that of fecal microbiota from men who have sex with women. We also demonstrated elevation of the gut homing marker CD103 (integrin αE) on CD4+ T cells by MSM-microbiota. Here we provide additional evidence that the gut microbiota is a risk factor for HIV transmission in MSM by showing elevated frequencies of the HIV co-receptor CCR5 on CD4+ T cells in human rectosigmoid colon biopsies. We discuss our interest in specific MSM-associated bacteria and propose the influx of CD103+ and CCR5+ CD4+ T cells into the colon as a potential link between the MSM microbiota and HIV transmission.
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Affiliation(s)
- Sara L. Coleman
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - C. Preston Neff
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Sam X. Li
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Abigail J.S. Armstrong
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Jennifer M. Schneider
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Sharon Sen
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Blair Fennimore
- Division of Gastroenterology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Thomas B. Campbell
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Catherine A. Lozupone
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Brent E. Palmer
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA,CONTACT Brent E. Palmer Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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Ni L, Song C, Wu X, Zhao X, Wang X, Li B, Gan Y. RNA-seq transcriptome profiling of porcine lung from two pig breeds in response to Mycoplasma hyopneumoniae infection. PeerJ 2019; 7:e7900. [PMID: 31656701 PMCID: PMC6812673 DOI: 10.7717/peerj.7900] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/16/2019] [Indexed: 12/12/2022] Open
Abstract
Background Mycoplasma hyopneumoniae (Mhp) is the main pathogen causing respiratory disease in the swine industry. Mhp infection rates differ across pig breeds, with Chinese native pig breeds that exhibit high fecundity (e.g., Jiangquhai, Meishan, Erhualian) more sensitive than Duroc, Landrace, and other imported pig breeds. However, the genetic basis of the immune response to Mhp infection in different pig breeds is largely unknown. Aims The aims of this study were to determine the relative Mhp susceptibility of the Chinese native Jiangquhai breed compared to the Duroc breed, and identify molecular mechanisms of differentially expressed genes (DEGs) using an RNA-sequencing (RNA-seq) approach. Methods Jiangquhai and Duroc pigs were artificially infected with the same Mhp dose. The entire experiment lasted 28 days. Daily weight gain, Mhp-specific antibody levels, and lung lesion scores were measured to evaluate the Mhp infection susceptibility of different breeds. Experimental pigs were slaughtered on the 28th day. Lung tissues were collected for total RNA extraction. RNA-seq was performed to identify DEGs, which were enriched by gene ontology (GO) and the Kyoto Encyclopedia annotation of Genes and Genomes (KEGG) databases. DEGs were validated with real-time quantitative polymerase chain reaction (RT-qPCR). Results Infection with the same Mhp dose produced a more serious condition in Jiangquhai pigs than in Duroc pigs. Jiangquhai pigs showed poorer growth, higher Mhp antibody levels, and more serious lung lesions compared with Duroc pigs. RNA-seq identified 2,250 and 3,526 DEGs in lung tissue from Jiangquhai and Duroc pigs, respectively. The two breeds shared 1,669 DEGs, which were involved in immune-relevant pathways including cytokine-cytokine receptor interaction, PI3K-Akt signaling pathway, and chemokine signaling pathway. Compared to Jiangquhai pigs, more chemokines, interferon response factors, and interleukins were specifically activated in Duroc pigs; CXCL10, CCL4, IL6 and IFNG genes were significantly up-regulated, which may help Duroc pigs enhance immune response and reduce Mhp susceptibility. Conclusion This study demonstrated differential immune-related DEGs in lung tissue from the two breeds, and revealed an important role of genetics in the immune response to Mhp infection. The biological functions of these important DEGs should be further confirmed and maybe applied as molecular markers that improve pig health.
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Affiliation(s)
- Ligang Ni
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China.,Department of Animal Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu, China
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xinsheng Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xuting Zhao
- Department of Animal Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu, China
| | - Xiaoyan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Bichun Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yuan Gan
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
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Transcriptome profile of lung dendritic cells after in vitro porcine reproductive and respiratory syndrome virus (PRRSV) infection. PLoS One 2017; 12:e0187735. [PMID: 29140992 PMCID: PMC5687707 DOI: 10.1371/journal.pone.0187735] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/25/2017] [Indexed: 12/02/2022] Open
Abstract
The porcine reproductive and respiratory syndrome (PRRS) is an infectious disease that leads to high financial and production losses in the global swine industry. The pathogenesis of this disease is dependent on a multitude of factors, and its control remains problematic. The immune system generally defends against infectious diseases, especially dendritic cells (DCs), which play a crucial role in the activation of the immune response after viral infections. However, the understanding of the immune response and the genetic impact on the immune response to PRRS virus (PRRSV) remains incomplete. In light of this, we investigated the regulation of the host immune response to PRRSV in porcine lung DCs using RNA-sequencing (RNA-Seq). Lung DCs from two different pig breeds (Pietrain and Duroc) were collected before (0 hours) and during various periods of infection (3, 6, 9, 12, and 24 hours post infection (hpi)). RNA-Seq analysis revealed a total of 20,396 predicted porcine genes, which included breed-specific differentially expressed immune genes. Pietrain and Duroc infected lung DCs showed opposite gene expression courses during the first time points post infection. Duroc lung DCs reacted more strongly and distinctly than Pietrain lung DCs during these periods (3, 6, 9, 12 hpi). Additionally, cluster analysis revealed time-dependent co-expressed groups of genes that were involved in immune-relevant pathways. Key clusters and pathways were identified, which help to explain the biological and functional background of lung DCs post PRRSV infection and suggest IL-1β1 as an important candidate gene. RNA-Seq was also used to characterize the viral replication of PRRSV for each breed. PRRSV was able to infect and to replicate differently in lung DCs between the two mentioned breeds. These results could be useful in investigations on immunity traits in pig breeding and enhancing the health of pigs.
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Paximadis M, Schramm DB, Gray GE, Sherman G, Coovadia A, Kuhn L, Tiemessen CT. Influence of intragenic CCL3 haplotypes and CCL3L copy number in HIV-1 infection in a sub-Saharan African population. Genes Immun 2013; 14:42-51. [PMID: 23151487 PMCID: PMC3554858 DOI: 10.1038/gene.2012.51] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 08/31/2012] [Accepted: 09/28/2012] [Indexed: 12/12/2022]
Abstract
Two CCL3 haplotypes (HapA1 and Hap-A3) and two polymorphic positions shared by the haplotypes (Hap-2SNP (single nucleotide polymorphism)) were investigated together with CCL3L copy number (CN), for their role in HIV-1 disease. Hap-A1 was associated with protection from in utero HIV-1 infection: exposed uninfected (EU) infants had higher representation of wild type (WT)/Hap-A1 than infected infants (excluding intrapartum (IP)-infected infants), which maintained significance post maternal Nevirapine (mNVP) and viral load (MVL) correction (P=0.04; odds ratio (OR)=0.33). Mother-infant pair analyses showed the protective effect of Hap-A1 is dependent on its presence in the infant. Hap-A3 was associated with increased IP transmission: WT/Hap-A3 was increased in IP-transmitting vs non-transmitting (NT) mothers, and remained significant post mNVP and MVL correction (P=0.02; OR=3.50). This deleterious effect of Hap-A3 seemed dependent on its presence in the mother. Hap-2SNP was associated with lower CD4 count in the NT mothers (P=0.03). CCL3 Hap-A1 was associated with high CCL3L CN in total (P=0.001) and EU infants (P=0.006); the effect was not additive, however, having either Hap-A1 or high CCL3L CN was more significantly (P=0.0008) associated with protection from in utero infection than Hap-A1 (P=0.028) or high CCL3L CN (P=0.002) alone. Linkage disequilibrium between Hap-A1 and high CCL3L CN appears unlikely given that a Nigerian population showed an opposite relationship.
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Affiliation(s)
- M Paximadis
- Centre for HIV and STIs: Cell Biology, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa.
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Kinetics of immune responses in deer mice experimentally infected with Sin Nombre virus. J Virol 2012; 86:10015-27. [PMID: 22787210 DOI: 10.1128/jvi.06875-11] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Deer mice are the principal reservoir hosts of Sin Nombre virus, the etiologic agent of most hantavirus cardiopulmonary syndrome cases in North America. Infection of deer mice results in persistence without conspicuous pathology, and most, if not all, infected mice remain infected for life, with periods of viral shedding. The kinetics of viral load, histopathology, virus distribution, and immune gene expression in deer mice were examined. Viral antigen was detected as early as 5 days postinfection and peaked on day 15 in the lungs, hearts, kidneys, and livers. Viral RNA levels varied substantially but peaked on day 15 in the lungs and heart, and antinucleocapsid IgG antibodies appeared in some animals on day 10, but a strong neutralizing antibody response failed to develop during the 20-day experiment. No clinical signs of disease were observed in any of the infected deer mice. Most genes were repressed on day 2, suggesting a typical early downregulation of gene expression often observed in viral infections. Several chemokine and cytokine genes were elevated, and markers of a T cell response occurred but then declined days later. Splenic transforming growth factor beta (TGF-β) expression was elevated early in infection, declined, and then was elevated again late in infection. Together, these data suggest that a subtle immune response that fails to clear the virus occurs in deer mice.
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Pan D, Das A, Liu D, Veazey RS, Pahar B. Isolation and characterization of intestinal epithelial cells from normal and SIV-infected rhesus macaques. PLoS One 2012; 7:e30247. [PMID: 22291924 PMCID: PMC3266894 DOI: 10.1371/journal.pone.0030247] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 12/15/2011] [Indexed: 01/14/2023] Open
Abstract
Impairment of intestinal epithelial barriers contributes to the progression of HIV/SIV infection and leads to generalized HIV-induced immune-cell activation during chronic infection. Rhesus macaques are the major animal model for studying HIV pathogenesis. However, detailed characterization of isolated rhesus epithelial cells (ECs) from intestinal tissues is not well defined. It is also not well documented whether isolated ECs had any other cell contaminants from intestinal tissues during the time of processing that might hamper interpretation of EC preparations or cultures. In this study, we identify and characterize ECs based on flow cytometry and immunohistochemistry methods using various enzymatic and mechanical isolation techniques to enrich ECs from intestinal tissues. This study shows that normal healthy ECs differentially express HLA-DR, CD23, CD27, CD90, CD95 and IL-10R markers. Early apoptosis and upregulation of ICAM-1 and HLA-DR in intestinal ECs are thought to be the key features in SIV mediated enteropathy. The data suggest that intestinal ECs might be playing an important role in mucosal immune responses by regulating the expression of different important regulatory and adhesion molecules and their function.
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Affiliation(s)
- Diganta Pan
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Arpita Das
- Division of Microbiology, Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - David Liu
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Ronald S. Veazey
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, Louisiana, United States of America
- Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Bapi Pahar
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, Louisiana, United States of America
- Tulane University School of Medicine, New Orleans, Louisiana, United States of America
- * E-mail:
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Abstract
Chemokines are small chemoattractant cytokines involved in homeostatic and inflammatory immune cell migration. These small proteins have multiple functional properties that extend beyond their most recognized role in controlling cellular migration. The complex immunobiology of chemokines, coupled with the use of subsets of chemokine receptors as HIV-1 and SIV entry co-receptors, suggests that these immunomodulators could play important roles in the pathogenesis associated with infection by HIV-1 or SIV. This review provides an overview of the effects of pathogenic infection on chemokine expression in the SIV/macaque model system, and outlines potential mechanisms by which changes in these expression profiles could contribute to development of disease. Key challenges faced in studying chemokine function in vivo and new opportunities for further study and development of therapeutic interventions are discussed. Continued growth in our understanding of the effects of pathogenic SIV infection on chemokine expression and function and the continuing development of chemokine receptor targeted therapeutics will provide the tools and the systems necessary for future studies of the roles of chemokines in HIV-1 pathogenesis.
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Affiliation(s)
- Todd A Reinhart
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, USA.
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