Infectious Diseases
Research Labs
The Andrews Lab
Control of Infectious Diseases in Resource-Limited Settings
Our laboratory aims to develop innovative approaches to the control of infectious diseases in resource-limited settings. Drawing upon the fields of epidemiology, microbiology and engineering, we strive to find solutions to extend the technologies that underlie diagnosis and treatment of infectious diseases to "last-mile" communities.
Publications
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The risk of tuberculosis in children after close exposure: a systematic review and individual-participant meta-analysis.
Lancet (London, England)
Martinez, L., Cords, O., Horsburgh, C. R., Andrews, J. R.
2020; 395 (10228): 973–84
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Abstract
Tens of millions of children are exposed to Mycobacterium tuberculosis globally every year; however, there are no contemporary estimates of the risk of developing tuberculosis in exposed children. The effectiveness of contact investigations and preventive therapy remains poorly understood.In this systematic review and meta-analysis, we investigated the development of tuberculosis in children closely exposed to a tuberculosis case and followed for incident disease. We restricted our search to cohort studies published between Jan 1, 1998, and April 6, 2018, in MEDLINE, Web of Science, BIOSIS, and Embase electronic databases. Individual-participant data and a pre-specified list of variables were requested from authors of all eligible studies. These included characteristics of the exposed child, the index case, and environmental characteristics. To be eligible for inclusion in the final analysis, a dataset needed to include: (1) individuals below 19 years of age; (2) follow-up for tuberculosis for a minimum of 6 months; (3) individuals with household or close exposure to an individual with tuberculosis; (4) information on the age and sex of the child; and (5) start and end follow-up dates. Studies assessing incident tuberculosis but without dates or time of follow-up were excluded. Our analysis had two primary aims: (1) estimating the risk of developing tuberculosis by time-period of follow-up, demographics (age, region), and clinical attributes (HIV, tuberculosis infection status, previous tuberculosis); and (2) estimating the effectiveness of preventive therapy and BCG vaccination on the risk of developing tuberculosis. We estimated the odds of prevalent tuberculosis with mixed-effects logistic models and estimated adjusted hazard ratios (HRs) for incident tuberculosis with mixed-effects Poisson regression models. The effectiveness of preventive therapy against incident tuberculosis was estimated through propensity score matching. The study protocol is registered with PROSPERO (CRD42018087022).In total, study groups from 46 cohort studies in 34 countries-29 (63%) prospective studies and 17 (37%) retrospective-agreed to share their data and were included in the final analysis. 137 647 tuberculosis-exposed children were evaluated at baseline and 130 512 children were followed for 429 538 person-years, during which 1299 prevalent and 999 incident tuberculosis cases were diagnosed. Children not receiving preventive therapy with a positive result for tuberculosis infection had significantly higher 2-year cumulative tuberculosis incidence than children with a negative result for tuberculosis infection, and this incidence was greatest among children below 5 years of age (19·0% [95% CI 8·4-37·4]). The effectiveness of preventive therapy was 63% (adjusted HR 0·37 [95% CI 0·30-0·47]) among all exposed children, and 91% (adjusted HR 0·09 [0·05-0·15]) among those with a positive result for tuberculosis infection. Among all children <5 years of age who developed tuberculosis, 83% were diagnosed within 90 days of the baseline visit.The risk of developing tuberculosis among exposed infants and young children is very high. Most cases occurred within weeks of contact investigation initiation and might not be preventable through prophylaxis. This suggests that alternative strategies for prevention are needed, such as earlier initiation of preventive therapy through rapid diagnosis of adult cases or community-wide screening approaches.National Institutes of Health.
View details for DOI 10.1016/S0140-6736(20)30166-5
View details for PubMedID 32199484
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Evaluating strategies for control of tuberculosis in prisons and prevention of spillover into communities: An observational and modeling study from Brazil.
PLoS medicine
Mabud, T. S., de Lourdes Delgado Alves, M., Ko, A. I., Basu, S., Walter, K. S., Cohen, T., Mathema, B., Colijn, C., Lemos, E., Croda, J., Andrews, J. R.
2019; 16 (1): e1002737
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Abstract
It has been hypothesized that prisons serve as amplifiers of general tuberculosis (TB) epidemics, but there is a paucity of data on this phenomenon and the potential population-level effects of prison-focused interventions. This study (1) quantifies the TB risk for prisoners as they traverse incarceration and release, (2) mathematically models the impact of prison-based interventions on TB burden in the general population, and (3) generalizes this model to a wide range of epidemiological contexts.We obtained individual-level incarceration data for all inmates (n = 42,925) and all reported TB cases (n = 5,643) in the Brazilian state of Mato Grosso do Sul from 2007 through 2013. We matched individuals between prisoner and TB databases and estimated the incidence of TB from the time of incarceration and the time of prison release using Cox proportional hazards models. We identified 130 new TB cases diagnosed during incarceration and 170 among individuals released from prison. During imprisonment, TB rates increased from 111 cases per 100,000 person-years at entry to a maximum of 1,303 per 100,000 person-years at 5.2 years. At release, TB incidence was 229 per 100,000 person-years, which declined to 42 per 100,000 person-years (the average TB incidence in Brazil) after 7 years. We used these data to populate a compartmental model of TB transmission and incarceration to evaluate the effects of various prison-based interventions on the incidence of TB among prisoners and the general population. Annual mass TB screening within Brazilian prisons would reduce TB incidence in prisons by 47.4% (95% Bayesian credible interval [BCI], 44.4%-52.5%) and in the general population by 19.4% (95% BCI 17.9%-24.2%). A generalized model demonstrates that prison-based interventions would have maximum effectiveness in reducing community incidence in populations with a high concentration of TB in prisons and greater degrees of mixing between ex-prisoners and community members. Study limitations include our focus on a single Brazilian state and our retrospective use of administrative databases.Our findings suggest that the prison environment, more so than the prison population itself, drives TB incidence, and targeted interventions within prisons could have a substantial effect on the broader TB epidemic.
View details for PubMedID 30677013
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Extensively Drug-Resistant Typhoid - Are Conjugate Vaccines Arriving Just in Time?
The New England journal of medicine
Andrews, J. R., Qamar, F. N., Charles, R. C., Ryan, E. T.
2018; 379 (16): 1493–95
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View details for PubMedID 30332569
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Typhoid conjugate vaccines: a new tool in the fight against antimicrobial resistance.
The Lancet. Infectious diseases
Andrews, J. R., Baker, S., Marks, F., Alsan, M., Garrett, D., Gellin, B. G., Saha, S. K., Qamar, F. N., Yousafzai, M. T., Bogoch, I. I., Antillon, M., Pitzer, V. E., Kim, J., John, J., Gauld, J., Mogasale, V., Ryan, E. T., Luby, S. P., Lo, N. C.
2018
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Abstract
Typhoid fever is an acute systemic infectious disease responsible for an estimated 12-20 million illnesses and over 150 000 deaths annually. In March, 2018, a new recommendation was issued by WHO for the programmatic use of typhoid conjugate vaccines in endemic countries. Health economic analyses of typhoid vaccines have informed funding decisions and national policies regarding vaccine rollout. However, by focusing only on averted typhoid cases and their associated costs, traditional cost-effectiveness analyses might underestimate crucial benefits of typhoid vaccination programmes, because the potential effect of typhoid vaccines on the treatment of patients with non-specific acute febrile illnesses is not considered. For every true case of typhoid fever, three to 25 patients without typhoid disease are treated with antimicrobials unnecessarily, conservatively amounting to more than 50 million prescriptions per year. Antimicrobials for suspected typhoid might therefore be an important selective pressure for the emergence and spread of antimicrobial resistance globally. We propose that large-scale, more aggressive typhoid vaccination programmes-including catch-up campaigns in children up to 15 years of age, and vaccination in lower incidence settings-have the potential to reduce the overuse of antimicrobials and thereby reduce antimicrobial resistance in many bacterial pathogens. Funding bodies and national governments must therefore consider the potential for broad reductions in antimicrobial use and resistance in decisions related to the rollout of typhoid conjugate vaccines.
View details for PubMedID 30170987
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Serial QuantiFERON testing and tuberculosis disease risk among young children: an observational cohort study.
The Lancet. Respiratory medicine
Andrews, J. R., Nemes, E., Tameris, M., Landry, B. S., Mahomed, H., McClain, J. B., Fletcher, H. A., Hanekom, W. A., Wood, R., McShane, H., Scriba, T. J., Hatherill, M.
2017
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Abstract
The value of quantitative interferon-γ release assay results for predicting progression from Mycobacterium tuberculosis infection to active disease is unknown. We aimed to investigate the relation between QuantiFERON-TB Gold In-Tube (QFT) conversion interferon-γ values and risk of subsequent active tuberculosis disease and of QFT reversion.We analysed data from a reported vaccine efficacy trial of the tuberculosis vaccine MVA85A in South Africa. QFT negative, HIV uninfected young children aged 18-24 weeks were enrolled. We stratified participants by quantitative QFT result (interferon-γ <0·35 IU/mL, 0·35-4·00 IU/mL, and >4·00 IU/mL) at the intermediate study visit (day 336) and determined risk of progression to active tuberculosis disease over the subsequent 6-24 months. No QFT differences were observed between placebo and MVA85A groups at day 336 or end of study; therefore, both groups were included in analyses. Study clinicians were not masked to QFT values, but strict case definitions were used that excluded QFT results. We used generalised additive models to evaluate the quantitative relation between day 336 QFT value and subsequent disease risk, and we compared disease rates between QFT strata using a two-sample Poisson test.Among 2512 young children with QFT tests done at day 336, 172 (7%) were positive; 87 (7%) of 1267 in placebo group and 85 (7%) of 1245 in the MVA85A group (p=1·00). Compared with QFT non-converters (tuberculosis disease incidence 0·7 per 100 person-years [95% CI 0·4-1·1]), children with QFT conversion at interferon-γ values between 0·35-4·00 IU/mL did not have significantly increased risk of disease (2·5 per 100 person-years [95% CI 0·4-9·4]; incidence rate ratio (IRR) 3·7 (95% CI 0·4-15·8; p=0·23). However, QFT conversion at interferon-γ values higher than 4·00 IU/mL was associated with substantially increased disease incidence (28·0 per 100 person-years [95% CI 14·9-45·7]) compared with non-converters (IRR 42·5 [95% CI 17·2-99·7]; p<0·0001), and compared with children with interferon-γ values between 0·35-4·00 IU/mL (IRR 11·4 [95% CI 2·4-107·2]; p=0·00047). Among 91 QFT converters who were given a repeat test, 53 (58%) reverted from positive to negative. QFT reversion risk was inversely associated with interferon-γ value at QFT conversion and was highest with interferon-γ values less than 4·00 IU/mL (47 [77%] of 61).In young children, tuberculosis disease risk was not significantly increased, and QFT reversion was common, following QFT conversion at interferon-γ values up to 10 times the recommended test threshold (0·35 IU/mL). By contrast, QFT conversion at very high interferon-γ values (>4·00 IU/mL) warrants intensified diagnostic and preventive intervention because of the extremely high risk of tuberculosis disease in these young children.Aeras, Wellcome Trust, and Oxford-Emergent Tuberculosis Consortium (OETC) were the funders of the MVA85A 020 Trial. National Institute of Allergy and Infectious Diseases supported this analysis.
View details for DOI 10.1016/S2213-2600(17)30060-7
View details for PubMedID 28215501
The Blish Lab
Defining Natural Immunity in Viral Disease
The Blish laboratory is in the Department of Medicine, Division of Infectious Diseases and Geographic Medicine and in the interdisciplinary Stanford Immunology program. Our goal is to develop new methods to prevent and control infectious diseases through better understanding of human immunology. We have several major areas of ongoing investigation.
Publications
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Progenitor identification and SARS-CoV-2 infection in human distal lung organoids.
Nature
Salahudeen, A. A., Choi, S. S., Rustagi, A., Zhu, J., van Unen, V., de la O, S. M., Flynn, R. A., Margalef-Catala, M., Santos, A. J., Ju, J., Batish, A., Usui, T., Zheng, G. X., Edwards, C. E., Wagar, L. E., Luca, V., Anchang, B., Nagendran, M., Nguyen, K., Hart, D. J., Terry, J. M., Belgrader, P., Ziraldo, S. B., Mikkelsen, T. S., Harbury, P. B., Glenn, J. S., Garcia, K. C., Davis, M. M., Baric, R. S., Sabatti, C., Amieva, M. R., Blish, C. A., Desai, T. J., Kuo, C. J.
2020
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Abstract
The distal lung contains terminal bronchioles and alveoli that facilitate gas exchange. Three-dimensional in vitro human distal lung culture systems would strongly facilitate investigation of pathologies including interstitial lung disease, cancer, and SARS-CoV-2-associated COVID-19 pneumonia. We generated long-term feeder-free, chemically defined culture of distal lung progenitors as organoids derived from single adult human alveolar epithelial type II (AT2) or KRT5+ basal cells. AT2 organoids exhibited AT1 transdifferentiation potential while basal cell organoids developed lumens lined by differentiated club and ciliated cells. Single cell analysis of basal organoid KRT5+ cells revealed a distinct ITGA6+ITGB4+ mitotic population whose proliferation further segregated to a TNFRSF12Ahi subfraction comprising ~10% of KRT5+ basal cells, residing in clusters within terminal bronchioles and exhibiting enriched clonogenic organoid growth activity. Distal lung organoids were created with apical-out polarity to display ACE2 on the exposed external surface, facilitating SARS-CoV-2 infection of AT2 and basal cultures and identifying club cells as a novel target population. This long-term, feeder-free organoid culture of human distal lung, coupled with single cell analysis, identifies unsuspected basal cell functional heterogeneity and establishes a facile in vitro organoid model for human distal lung infections including COVID-19-associated pneumonia.
View details for DOI 10.1038/s41586-020-3014-1
View details for PubMedID 33238290
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Mass Cytometry Analysis of the NK Cell Receptor-Ligand Repertoire Reveals Unique Differences between Dengue-Infected Children and Adults.
ImmunoHorizons
McKechnie, J. L., Beltran, D., Ferreira, A. M., Vergara, R., Saenz, L., Vergara, O., Estripeaut, D., Arauz, A. B., Simpson, L. J., Holmes, S., Lopez-Verges, S., Blish, C. A.
2020; 4 (10): 634–47
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Abstract
Dengue virus (DENV) is a significant cause of morbidity in many regions of the world, with children at the greatest risk of developing severe dengue. NK cells, characterized by their ability to rapidly recognize and kill virally infected cells, are activated during acute DENV infection. However, their role in viral clearance versus pathogenesis has not been fully elucidated. Our goal was to profile the NK cell receptor-ligand repertoire to provide further insight into the function of NK cells during pediatric and adult DENV infection. We used mass cytometry to phenotype isolate NK cells and PBMCs from a cohort of DENV-infected children and adults. Using unsupervised clustering, we found that pediatric DENV infection leads to a decrease in total NK cell frequency with a reduction in the percentage of CD56dimCD38bright NK cells and an increase in the percentage of CD56dimperforinbright NK cells. No such changes were observed in adults. Next, we identified markers predictive of DENV infection using a differential state test. In adults, NK cell expression of activation markers, including CD69, perforin, and Fas-L, and myeloid cell expression of activating NK cell ligands, namely Fas, were predictive of infection. In contrast, increased NK cell expression of the maturation marker CD57 and myeloid cell expression of inhibitory ligands, such as HLA class I molecules, were predictive of pediatric DENV infection. These findings suggest that acute pediatric DENV infection may result in diminished NK cell activation, which could contribute to enhanced pathogenesis and disease severity.
View details for DOI 10.4049/immunohorizons.2000074
View details for PubMedID 33067399
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Cytokine profile in plasma of severe COVID-19 does not differ from ARDS and sepsis.
JCI insight
Wilson, J. G., Simpson, L. J., Ferreira, A., Rustagi, A., Roque, J. A., Asuni, A., Ranganath, T., Grant, P. M., Subramanian, A. K., Rosenberg-Hasson, Y., Maecker, H., Holmes, S., Levitt, J. E., Blish, C., Rogers, A. J.
2020
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Abstract
BACKGROUND: Elevated levels of inflammatory cytokines have been associated with poor outcomes among COVID-19 patients. It is unknown, however, how these levels compare to those observed in critically ill patients with ARDS or sepsis due to other causes.METHODS: We used a luminex assay to determine expression of 76 cytokines from plasma of hospitalized COVID-19 patients and banked plasma samples from ARDS and sepsis patients. Our analysis focused on detecting statistical differences in levels of 6 cytokines associated with cytokine storm (IL-1b, IL-1RA, IL-6, IL-8, IL-18, and TNFalpha) between patients with moderate COVID-19, severe COVID-19, and ARDS or sepsis.RESULTS: 15 hospitalized COVID-19 patients, 9 of whom were critically ill, were compared to critically ill patients with ARDS (n = 12) or sepsis (n = 16). There were no statistically significant differences in baseline levels of IL-1b, IL-1RA, IL-6, IL-8, IL-18, and TNFalpha between patients with COVID-19 and critically ill controls with ARDS or sepsis.CONCLUSIONS: Levels of inflammatory cytokines were not higher in severe COVID-19 patients than in moderate COVID-19 or critically ill patients with ARDS or sepsis in this small cohort. Broad use of immunosuppressive therapies in ARDS has failed in numerous Phase 3 studies; use of these therapies in unselected patients with COVID-19 may be unwarranted.FUNDING: A.J.R.: Stanford ICU Biobank NHLBI K23 HL125663. C.A.B.: Burroughs Wellcome Fund Investigators in the Pathogenesis of Infectious Diseases #1016687; NIH/NIAID U19AI057229-16 (PI MM Davis); Stanford Maternal Child Health Research Institute; Chan Zuckerberg Biohub.
View details for DOI 10.1172/jci.insight.140289
View details for PubMedID 32706339
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A single-cell atlas of the peripheral immune response in patients with severe COVID-19.
Nature medicine
Wilk, A. J., Rustagi, A., Zhao, N. Q., Roque, J., Martinez-Colon, G. J., McKechnie, J. L., Ivison, G. T., Ranganath, T., Vergara, R., Hollis, T., Simpson, L. J., Grant, P., Subramanian, A., Rogers, A. J., Blish, C. A.
2020
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Abstract
There is an urgent need to better understand the pathophysiology of Coronavirus disease 2019 (COVID-19), the global pandemic caused by SARS-CoV-2, which has infected more than three million people worldwide1. Approximately 20% of patients with COVID-19 develop severe disease and 5% of patients require intensive care2. Severe disease has been associated with changes in peripheral immune activity, including increased levels of pro-inflammatory cytokines3,4 that may be produced by a subset of inflammatory monocytes5,6, lymphopenia7,8 and T cell exhaustion9,10. To elucidate pathways in peripheral immune cells that might lead to immunopathology or protective immunity in severe COVID-19, we applied single-cell RNA sequencing (scRNA-seq) to profile peripheral blood mononuclear cells (PBMCs) from seven patients hospitalized for COVID-19, four of whom had acute respiratory distress syndrome, and six healthy controls. We identify reconfiguration of peripheral immune cell phenotype in COVID-19, including a heterogeneous interferon-stimulated gene signature, HLA class II downregulation and a developing neutrophil population that appears closely related to plasmablasts appearing in patients with acute respiratory failure requiring mechanical ventilation. Importantly, we found that peripheral monocytes and lymphocytes do not express substantial amounts of pro-inflammatory cytokines. Collectively, we provide a cell atlas of the peripheral immune response to severe COVID-19.
View details for DOI 10.1038/s41591-020-0944-y
View details for PubMedID 32514174
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Enhancing natural killer cell function with gp41-targeting bispecific antibodies to combat HIV infection.
AIDS (London, England)
Ramadoss, N. S., Zhao, N. Q., Richardson, B. A., Grant, P. M., Kim, P. S., Blish, C. A.
2020
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Abstract
OBJECTIVE(S): To develop and evaluate the activity of bispecific antibodies (bsAbs) to enhance NK cell antibody-dependent cellular cytotoxicity (ADCC) against HIV-infected cells.DESIGN: These bsAbs are based on patient-derived antibodies targeting the conserved gp41 stump of HIV Env, and also incorporate a high affinity single chain variable fragment (scFv) targeting the activating receptor CD16 on NK cells. Overall, we expect the bsAbs to provide increased affinity and avidity over their corresponding monoclonal antibodies, allowing for improved ADCC activity against Env-expressing target cells.METHODS: bsAbs and their corresponding mAbs were expressed in 293T cells and purified. The binding of bsAbs and mAbs to their intended targets was determined using Bio-Layer Interferometry, as well as flow cytometry-based binding assays on in vitro infected cells. The ability of these bsAbs to improve NK cell activity against HIV-infected cells was tested using in vitro co-culture assays, using flow cytometry and calcein release to analyze NK cell degranulation and target cell killing, respectively.RESULTS: The bsAbs bound gp41 with similar affinity to their corresponding mAbs, and had increased affinity for CD16. The bsAbs also bound to primary CD4 T cells infected in vitro with two different strains of HIV. In addition, the bsAbs induce increased NK cell degranulation and killing of autologous HIV-infected CD4 T cells.CONCLUSIONS: Based on their in vitro killing efficacy, bsAbs may provide a promising strategy to improve NK-mediated immune targeting of infected cells during HIV infection.
View details for DOI 10.1097/QAD.0000000000002543
View details for PubMedID 32287071
The Bollyky Lab
Immune Responses in Injured and Infected Tissues
Our lab studies how immune responses are regulated within injured and infected tissues. We work at the intersection of immunology, structural biology, bioengineering, and microbiology. Our goals are to understand the factors that drive chronic inflammation and to develop novel therapeutics to promote wound healing and immune tolerance.
Publications
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Filamentous bacteriophages are associated with chronic Pseudomonas lung infections and antibiotic resistance in cystic fibrosis
SCIENCE TRANSLATIONAL MEDICINE
Burgener, E. B., Sweere, J. M., Bach, M. S., Secor, P. R., Haddock, N., Jennings, L. K., Marvig, R. L., Johansen, H., Rossi, E., Cao, X., Tian, L., Nedelec, L., Molin, S., Bollyky, P. L., Milla, C. E.
2019; 11 (488)
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View details for DOI 10.1126/scitranslmed.aau9748
View details for Web of Science ID 000465116400003
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Bacteriophage trigger antiviral immunity and prevent clearance of bacterial infection.
Science (New York, N.Y.)
Sweere, J. M., Van Belleghem, J. D., Ishak, H., Bach, M. S., Popescu, M., Sunkari, V., Kaber, G., Manasherob, R., Suh, G. A., Cao, X., de Vries, C. R., Lam, D. N., Marshall, P. L., Birukova, M., Katznelson, E., Lazzareschi, D. V., Balaji, S., Keswani, S. G., Hawn, T. R., Secor, P. R., Bollyky, P. L.
2019; 363 (6434)
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Abstract
Bacteriophage are abundant at sites of bacterial infection, but their effects on mammalian hosts are unclear. We have identified pathogenic roles for filamentous Pf bacteriophage produced by Pseudomonas aeruginosa (Pa) in suppression of immunity against bacterial infection. Pf promote Pa wound infection in mice and are associated with chronic human Pa wound infections. Murine and human leukocytes endocytose Pf, and internalization of this single-stranded DNA virus results in phage RNA production. This triggers Toll-like receptor 3 (TLR3)- and TIR domain-containing adapter-inducing interferon-β (TRIF)-dependent type I interferon production, inhibition of tumor necrosis factor (TNF), and the suppression of phagocytosis. Conversely, immunization of mice against Pf prevents Pa wound infection. Thus, Pf triggers maladaptive innate viral pattern-recognition responses, which impair bacterial clearance. Vaccination against phage virions represents a potential strategy to prevent bacterial infection.
View details for PubMedID 30923196
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Interactions between Bacteriophage, Bacteria, and the Mammalian Immune System.
Viruses
Van Belleghem, J. D., Dąbrowska, K., Vaneechoutte, M., Barr, J. J., Bollyky, P. L.
2018; 11 (1)
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Abstract
The human body is host to large numbers of bacteriophages (phages)⁻a diverse group of bacterial viruses that infect bacteria. Phage were previously regarded as bystanders that only impacted immunity indirectly via effects on the mammalian microbiome. However, it has become clear that phages also impact immunity directly, in ways that are typically anti-inflammatory. Phages can modulate innate immunity via phagocytosis and cytokine responses, but also impact adaptive immunity via effects on antibody production and effector polarization. Phages may thereby have profound effects on the outcome of bacterial infections by modulating the immune response. In this review we highlight the diverse ways in which phages interact with human cells. We present a computational model for predicting these complex and dynamic interactions. These models predict that the phageome may play important roles in shaping mammalian-bacterial interactions.
View details for PubMedID 30585199
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Hyaluronan synthesis is necessary for autoreactive T-cell trafficking, activation, and Th1 polarization.
Proceedings of the National Academy of Sciences of the United States of America
Kuipers, H. F., Rieck, M., Gurevich, I., Nagy, N., Butte, M. J., Negrin, R. S., Wight, T. N., Steinman, L., Bollyky, P. L.
2016; 113 (5): 1339-1344
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Abstract
The extracellular matrix polysaccharide hyaluronan (HA) accumulates at sites of autoimmune inflammation, including white matter lesions in multiple sclerosis (MS), but its functional importance in pathogenesis is unclear. We have evaluated the impact of 4-methylumbelliferone (4-MU), an oral inhibitor of HA synthesis, on disease progression in the experimental autoimmune encephalomyelitis (EAE) mouse model of MS. Treatment with 4-MU decreases the incidence of EAE, delays its onset, and reduces the severity of established disease. 4-MU inhibits the activation of autoreactive T cells and prevents their polarization toward a Th1 phenotype. Instead, 4-MU promotes polarization toward a Th2 phenotpye and induction of Foxp3(+) regulatory T cells. Further, 4-MU hastens trafficking of T cells through secondary lymphoid organs, impairs the infiltration of T cells into the CNS parenchyma, and limits astrogliosis. Together, these data suggest that HA synthesis is necessary for disease progression in EAE and that treatment with 4-MU may be a potential therapeutic strategy in CNS autoimmunity. Considering that 4-MU is already a therapeutic, called hymecromone, that is approved to treat biliary spasm in humans, we propose that it could be repurposed to treat MS.
View details for DOI 10.1073/pnas.1525086113
View details for PubMedID 26787861
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Filamentous Bacteriophage Promote Biofilm Assembly and Function
CELL HOST & MICROBE
Secor, P. R., Sweere, J. M., Michaels, L. A., Malkovskiy, A. V., Lazzareschi, D., Katznelson, E., Rajadas, J., Birnbaum, M. E., Arrigoni, A., Braun, K. R., Evanko, S. P., Stevens, D. A., Kaminsky, W., Singh, P. K., Parks, W. C., Bollyky, P. L.
2015; 18 (5): 549-559
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Abstract
Biofilms-communities of bacteria encased in a polymer-rich matrix-confer bacteria with the ability to persist in pathologic host contexts, such as the cystic fibrosis (CF) airways. How bacteria assemble polymers into biofilms is largely unknown. We find that the extracellular matrix produced by Pseudomonas aeruginosa self-assembles into a liquid crystal through entropic interactions between polymers and filamentous Pf bacteriophages, which are long, negatively charged filaments. This liquid crystalline structure enhances biofilm function by increasing adhesion and tolerance to desiccation and antibiotics. Pf bacteriophages are prevalent among P. aeruginosa clinical isolates and were detected in CF sputum. The addition of Pf bacteriophage to sputum polymers or serum was sufficient to drive their rapid assembly into viscous liquid crystals. Fd, a related bacteriophage of Escherichia coli, has similar biofilm-building capabilities. Targeting filamentous bacteriophage or the liquid crystalline organization of the biofilm matrix may represent antibacterial strategies.
View details for DOI 10.1016/j.chom.2015.10.013
View details for Web of Science ID 000365113100008
View details for PubMedID 26567508
View details for PubMedCentralID PMC4653043
The Einav Lab
Understanding Virus-Host Protein Interactions
The goals of our lab are to better understand virus-host protein interactions, identify host proteins or pathways required by multiple viruses, and translate this knowledge into the development of novel, broad-spectrum, host-centered antiviral approaches with a high genetic barrier for resistance.
Publications
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BIKE regulates dengue virus infection and is a cellular target for broad-spectrum antivirals.
Antiviral research
Pu, S., Schor, S., Karim, M., Saul, S., Robinson, M., Kumar, S., Prugar, L. I., Dorosky, D. E., Brannan, J., Dye, J. M., Einav, S.
2020: 104966
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Abstract
Global health is threatened by emerging viruses, many of which lack approved therapies and effective vaccines, including dengue, Ebola, and Venezuelan equine encephalitis. We previously reported that AAK1 and GAK, two of the four members of the understudied Numb-associated kinases (NAK) family, control intracellular trafficking of RNA viruses. Nevertheless, the role of BIKE and STK16 in viral infection remained unknown. Here, we reveal a requirement for BIKE, but not STK-16, in dengue virus (DENV) infection. BIKE mediates both early (postinternalization) and late (assembly/egress) stages in the DENV life cycle, and this effect is mediated in part by phosphorylation of a threonine 156 (T156) residue in the mu subunit of the adaptor protein (AP) 2 complex. Pharmacological compounds with potent anti-BIKE activity, including the investigational anticancer drug 5Z-7-oxozeaenol and more selective inhibitors, suppress DENV infection both in vitro and ex vivo. BIKE overexpression reverses the antiviral activity, validating that the mechanism of antiviral action is, at least in part, mediated by BIKE. Lastly, 5Z-7-oxozeaenol exhibits antiviral activity against viruses from three unrelated RNA viral families with a high genetic barrier to resistance. These findings reveal regulation of poorly understood stages of the DENV life cycle via BIKE signaling and establish a proof-of-principle that pharmacological inhibition of BIKE can be potentially used as a broad-spectrum strategy against acute emerging viral infections.
View details for DOI 10.1016/j.antiviral.2020.104966
View details for PubMedID 33137362
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Potent antiviral activity of novel multi-substituted 4-anilinoquin(az)olines.
Bioorganic & medicinal chemistry letters
Saul, S., Pu, S., Zuercher, W. J., Einav, S., Asquith, C. R.
2020; 30 (16): 127284
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Abstract
Screening a series of 4-anilinoquinolines and 4-anilinoquinazolines enabled identification of potent novel inhibitors of dengue virus (DENV). Preparation of focused 4-anilinoquinoline/quinazoline scaffold arrays led to the identification of a series of high potency 6-substituted bromine and iodine derivatives. The most potent compound 6-iodo-4-((3,4,5-trimethoxyphenyl)amino)quinoline-3-carbonitrile (47) inhibited DENV infection with an EC50=79nM. Crucially, these compounds showed very limited toxicity with CC50 values >10M in almost all cases. This new promising series provides an anchor point for further development to optimize compound properties.
View details for DOI 10.1016/j.bmcl.2020.127284
View details for PubMedID 32631507
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Towards Predicting Progression to Severe Dengue.
Trends in microbiology
Robinson, M., Einav, S.
2020
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Abstract
There is an urgent need for prognostic assays to predict progression to severe dengue infection, which is a major global threat. While the majority of symptomatic dengue patients experience an acute febrile illness, 5-20% progress to severe infection associated with significant morbidity and mortality. Early monitoring and administration of supportive care reduce mortality and clinically usable biomarkers to predict severe dengue are needed. Here, we review recent discoveries of gene sets, anti-dengue antibody properties, and inflammatory markers with potential utility as predictors of disease progression. Upon larger scale validation and development of affordable sample-to-answer technologies, some of these biomarkers may be utilized to develop the first prognostic assay for improving patient care and allocating healthcare resources more effectively in dengue endemic countries.
View details for DOI 10.1016/j.tim.2019.12.003
View details for PubMedID 31982232
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Old Drugs for a New Virus: Repurposed Approaches for Combating COVID-19.
ACS infectious diseases
Saul, S., Einav, S.
2020
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Abstract
There is a large global unmet need for effective countermeasures to combat severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19). The development of novel antiviral drugs is expensive and too slow to meet the immediate need. The repurposing of drugs that are approved or are under advanced clinical investigation provides a cost- and time-effective therapeutic solution. This review summarizes the major repurposed approaches that have been proposed or are already being studied in clinical trials for COVID-19. Among these approaches are drugs that aim to reduce SARS-CoV-2 replication by targeting either viral enzymatic functions or cellular factors required for the viral life cycle. Drugs that modulate the host immune response to SARS-CoV-2 infection by boosting it to enhance viral clearance or by suppressing it to prevent excessive inflammation and tissue injury represent another category. Lastly, we discuss means to discover repurposed drugs and the ongoing challenges associated with the off-label use of existing drugs in the context of the COVID-19 outbreak.
View details for DOI 10.1021/acsinfecdis.0c00343
View details for PubMedID 32687696
View details for PubMedCentralID PMC7416635
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Broadly neutralizing human antibodies against dengue virus identified by single B cell transcriptomics.
eLife
Durham, N. D., Agrawal, A., Waltari, E., Croote, D., Zanini, F., Fouch, M., Davidson, E., Smith, O., Carabajal, E., Pak, J. E., Doranz, B. J., Robinson, M., Sanz, A. M., Albornoz, L. L., Rosso, F., Einav, S., Quake, S. R., McCutcheon, K. M., Goo, L.
2019; 8
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Abstract
Eliciting broadly neutralizing antibodies (bNAbs) against the four dengue virus serotypes (DENV1-4) that are spreading into new territories is an important goal of vaccine design. To define bNAb targets, we characterized 28 antibodies belonging to expanded and hypermutated clonal families identified by transcriptomic analysis of single plasmablasts from DENV-infected individuals. Among these, we identified J9 and J8, two somatically related bNAbs that potently neutralized DENV1-4. Mutagenesis studies showed that the major recognition determinants of these bNAbs are in E protein domain I, distinct from the only known class of human bNAbs against DENV with a well-defined epitope. B cell repertoire analysis from acute-phase peripheral blood suggested that J9 and J8 followed divergent somatic hypermutation pathways, and that a limited number of mutations was sufficient for neutralizing activity. Our study suggests multiple B cell evolutionary pathways leading to DENV bNAbs targeting a new epitope that can be exploited for vaccine design.
View details for DOI 10.7554/eLife.52384
View details for PubMedID 31820734
Jagannathan Lab
Translational Immunology Focused on Malaria-Specific Immune Responses
The goals of this laboratory are to further our understanding of the correlates and mechanisms of clinical immunity to malaria through field-based studies, and to better understand the immunologic consequences of malaria control interventions.
These studies bridge immune profiling techniques including multiparameter flow cytometry, transcriptomics, epigenetics, and multiplex antibody profiling to epidemiologic studies of antimalarial immunity in children.
Publications
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Intermittent preventive treatment with dihydroartemisinin-piperaquine and risk of malaria following cessation in young Ugandan children: a double-blind, randomised, controlled trial.
The Lancet. Infectious diseases
Muhindo, M. K., Jagannathan, P., Kakuru, A., Opira, B., Olwoch, P., Okiring, J., Nalugo, N., Clark, T. D., Ruel, T., Charlebois, E., Feeney, M. E., Havlir, D. V., Dorsey, G., Kamya, M. R.
2019
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Abstract
BACKGROUND: Intermittent preventive treatment (IPT) of malaria with dihydroartemisinin-piperaquine is a promising strategy for malaria prevention in young African children. However, the optimal dosing strategy is unclear and conflicting evidence exists regarding the risk of malaria after cessation of chemoprevention. We aimed to compare two dosing strategies of IPT with dihydroartemisinin-piperaquine in young Ugandan children, and to evaluate the risk of malaria after cessation of IPT.METHODS: In this double-blind, randomised controlled phase 2 trial, women and their unborn children were recruited at Tororo District Hospital (Tororo, Uganda). Eligible participants were HIV-negative women aged 16 years or older with a viable pregnancy (gestational age 12-20 weeks). Women and their unborn children were randomly assigned (1:1:1:1) to one of four treatment groups, all receiving dihydroartemisinin-piperaquine, on the basis of the IPT intervention received by the woman during pregnancy: women every 8 weeks, children every 4 weeks; women every 4 weeks, children every 4 weeks; women every 8 weeks, children every 12 weeks; and women every 4 weeks, children every 12 weeks. Block randomisation was done by an independent investigator using a computer-generated randomisation list (permuted block sizes of six and 12). We analysed children on the basis of their random assignment to receive dihydroartemisinin-piperaquine (20 mg/160 mg tablets) once daily for 3 consecutive days every 4 weeks or 12 weeks. Children received study drugs from age 8 weeks to 24 months and were followed-up to age 36 months. Participants and investigators were masked to treatment allocation. The primary outcome was the incidence of symptomatic malaria during the intervention and following cessation of the intervention, adjusted for potential confounders. The primary outcome and safety were assessed in the modified intention-to-treat population, which included all children who reached 8 weeks of age and received at least one dose of study drug. This trial is registered with ClinicalTrials.gov, number NCT02163447.FINDINGS: Between Oct 21, 2014, and May 18, 2015, 191 children were born, of whom 183 reached 8 weeks of age and received at least one dose of study drug and thus were included in the primary analysis (96 children in the 4-week group and 87 in the 12-week group). During the intervention, the incidence of symptomatic malaria was significantly lower among children treated every 4 weeks than children treated every 12 weeks; three episodes occurred among children treated every 4 weeks (incidence 0·018 episodes per person-year) compared with 61 episodes among children treated every 12 weeks (incidence 0·39 episodes per person-year; adjusted incidence rate ratio [aIRR] 0·041, 95% CI 0·012-0·150, p<0·0001). After cessation of IPT, children who had previously received dihydroartemisinin-piperaquine every 4 weeks had a lower incidence of symptomatic malaria than children who were treated every 12 weeks; 62 episodes occurred among children previously treated every 4 weeks (incidence 0·73 episodes per person-year) compared with 83 episodes among children treated every 12 weeks (incidence 1·1 episodes per person-year; aIRR 0·62, 0·40-0·95, p=0·028). In the 4-week group, 94 (98%) of 96 children had adverse events versus 87 (100%) of 87 children in the 12-week group. The most commonly reported adverse event was cough in both treatment groups (94 [98%] in the 4-week group vs 87 [100%] in the 12-week group). 16 children had severe adverse events (seven [7%] children in the 4-week group vs nine [10%] children in the 12-week group). No severe adverse events were thought to be related to study drug administration. One death occurred during the intervention (age 8 weeks to 24 months), which was due to respiratory failure unrelated to malaria.INTERPRETATION: IPT with dihydroartemisinin-piperaquine given every 4 weeks was superior to treatment every 12 weeks for the prevention of malaria during childhood, and this protection was extended for up to 1 year after cessation of IPT.FUNDING: Eunice Kennedy Shriver National Institute of Child Health and Human Development.
View details for DOI 10.1016/S1473-3099(19)30299-3
View details for PubMedID 31307883
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Dihydroartemisinin-piperaquine for intermittent preventive treatment of malaria during pregnancy and risk of malaria in early childhood: A randomized controlled trial.
PLoS medicine
Jagannathan, P., Kakuru, A., Okiring, J., Muhindo, M. K., Natureeba, P., Nakalembe, M., Opira, B., Olwoch, P., Nankya, F., Ssewanyana, I., Tetteh, K., Drakeley, C., Beeson, J., Reiling, L., Clark, T. D., Rodriguez-Barraquer, I., Greenhouse, B., Wallender, E., Aweeka, F., Prahl, M., Charlebois, E. D., Feeney, M. E., Havlir, D. V., Kamya, M. R., Dorsey, G.
2018; 15 (7): e1002606
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Abstract
BACKGROUND: Intermittent preventive treatment of malaria in pregnancy (IPTp) with dihydroartemisinin-piperaquine (IPTp-DP) has been shown to reduce the burden of malaria during pregnancy compared to sulfadoxine-pyrimethamine (IPTp-SP). However, limited data exist on how IPTp regimens impact malaria risk during infancy. We conducted a double-blinded randomized controlled trial (RCT) to test the hypothesis that children born to mothers given IPTp-DP would have a lower incidence of malaria during infancy compared to children born to mothers who received IPTp-SP.METHODS AND FINDINGS: We compared malaria metrics among children in Tororo, Uganda, born to women randomized to IPTp-SP given every 8 weeks (SP8w, n = 100), IPTp-DP every 8 weeks (DP8w, n = 44), or IPTp-DP every 4 weeks (DP4w, n = 47). After birth, children were given chemoprevention with DP every 12 weeks from 8 weeks to 2 years of age. The primary outcome was incidence of malaria during the first 2 years of life. Secondary outcomes included time to malaria from birth and time to parasitemia following each dose of DP given during infancy. Results are reported after adjustment for clustering (twin gestation) and potential confounders (maternal age, gravidity, and maternal parasitemia status at enrolment).The study took place between June 2014 and May 2017. Compared to children whose mothers were randomized to IPTp-SP8w (0.24 episodes per person year [PPY]), the incidence of malaria was higher in children born to mothers who received IPTp-DP4w (0.42 episodes PPY, adjusted incidence rate ratio [aIRR] 1.92; 95% CI 1.00-3.65, p = 0.049) and nonsignificantly higher in children born to mothers who received IPT-DP8w (0.30 episodes PPY, aIRR 1.44; 95% CI 0.68-3.05, p = 0.34). However, these associations were modified by infant sex. Female children whose mothers were randomized to IPTp-DP4w had an apparently 4-fold higher incidence of malaria compared to female children whose mothers were randomized to IPTp-SP8w (0.65 versus 0.20 episodes PPY, aIRR 4.39, 95% CI 1.87-10.3, p = 0.001), but no significant association was observed in male children (0.20 versus 0.28 episodes PPY, aIRR 0.66, 95% CI 0.25-1.75, p = 0.42). Nonsignificant increases in malaria incidence were observed among female, but not male, children born to mothers who received DP8w versus SP8w. In exploratory analyses, levels of malaria-specific antibodies in cord blood were similar between IPTp groups and sex. However, female children whose mothers were randomized to IPTp-DP4w had lower mean piperaquine (PQ) levels during infancy compared to female children whose mothers received IPTp-SP8w (coef 0.81, 95% CI 0.65-1.00, p = 0.048) and male children whose mothers received IPTp-DP4w (coef 0.72, 95% CI 0.57-0.91, p = 0.006). There were no significant sex-specific differences in PQ levels among children whose mothers were randomized to IPTp-SP8w or IPTp-DP8w. The main limitations were small sample size and childhood provision of DP every 12 weeks in infancy.CONCLUSIONS: Contrary to our hypothesis, preventing malaria in pregnancy with IPTp-DP in the context of chemoprevention with DP during infancy does not lead to a reduced incidence of malaria in childhood; in this setting, it may be associated with an increased incidence of malaria in females. Future studies are needed to better understand the biological mechanisms of in utero drug exposure on drug metabolism and how this may affect the dosing of antimalarial drugs for treatment and prevention during infancy.TRIAL REGISTRATION: ClinicalTrials.gov number NCT02163447.
View details for PubMedID 30016328
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Vδ2+ T cell response to malaria correlates with protection from infection but is attenuated with repeated exposure.
Scientific reports
Jagannathan, P., Lutwama, F., Boyle, M. J., Nankya, F., Farrington, L. A., McIntyre, T. I., Bowen, K., Naluwu, K., Nalubega, M., Musinguzi, K., Sikyomu, E., Budker, R., Katureebe, A., Rek, J., Greenhouse, B., Dorsey, G., Kamya, M. R., Feeney, M. E.
2017; 7 (1): 11487
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Abstract
Vδ2(+) γδ T cells are semi-innate T cells that expand markedly following P. falciparum (Pf) infection in naïve adults, but are lost and become dysfunctional among children repeatedly exposed to malaria. The role of these cells in mediating clinical immunity (i.e. protection against symptoms) to malaria remains unclear. We measured Vδ2(+) T cell absolute counts at acute and convalescent malaria timepoints (n = 43), and Vδ2(+) counts, cellular phenotype, and cytokine production following in vitro stimulation at asymptomatic visits (n = 377), among children aged 6 months to 10 years living in Uganda. Increasing age was associated with diminished in vivo expansion following malaria, and lower Vδ2 absolute counts overall, among children living in a high transmission setting. Microscopic parasitemia and expression of the immunoregulatory markers Tim-3 and CD57 were associated with diminished Vδ2(+) T cell pro-inflammatory cytokine production. Higher Vδ2 pro-inflammatory cytokine production was associated with protection from subsequent Pf infection, but also with an increased odds of symptoms once infected. Vδ2(+) T cells may play a role in preventing malaria infection in children living in endemic settings; progressive loss and dysfunction of these cells may represent a disease tolerance mechanism that contributes to the development of clinical immunity to malaria.
View details for PubMedID 28904345
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Effective Antimalarial Chemoprevention in Childhood Enhances the Quality of CD4(+) T Cells and Limits Their Production of Immunoregulatory Interleukin 10
JOURNAL OF INFECTIOUS DISEASES
Jagannathan, P., Bowen, K., Nankya, F., McIntyre, T. I., Auma, A., Wamala, S., Sikyomu, E., Naluwu, K., Nalubega, M., Boyle, M. J., Farrington, L. A., Bigira, V., Kapisi, J., Aweeka, F., Greenhouse, B., Kamya, M., Dorsey, G., Feeney, M. E.
2016; 214 (2): 329-338
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Abstract
Experimental inoculation of viable Plasmodium falciparum sporozoites administered with chemoprevention targeting blood-stage parasites results in protective immunity. It is unclear whether chemoprevention similarly enhances immunity following natural exposure to malaria.We assessed P. falciparum-specific T-cell responses among Ugandan children who were randomly assigned to receive monthly dihydroartemisinin-piperaquine (DP; n = 87) or no chemoprevention (n = 90) from 6 to 24 months of age, with pharmacologic assessments for adherence, and then clinically followed for an additional year.During the intervention, monthly DP reduced malaria episodes by 55% overall (P < .001) and by 97% among children who were highly adherent to DP (P < .001). In the year after the cessation of chemoprevention, children who were highly adherent to DP had a 55% reduction in malaria incidence as compared to children given no chemoprevention (P = .004). Children randomly assigned to receive DP had higher frequencies of blood-stage specific CD4(+) T cells coproducing interleukin-2 and tumor necrosis factor α (P = .003), which were associated with protection from subsequent clinical malaria and parasitemia, and fewer blood-stage specific CD4(+) T cells coproducing interleukin-10 and interferon γ (P = .001), which were associated with increased risk of malaria.In this setting, effective antimalarial chemoprevention fostered the development of CD4(+) T cells that coproduced interleukin 2 and tumor necrosis factor α and were associated with prospective protection, while limiting CD4(+) T-cell production of the immunoregulatory cytokine IL-10.
View details for DOI 10.1093/infdis/jiw147
View details for Web of Science ID 000379822900021
View details for PubMedID 27067196
View details for PubMedCentralID PMC4918829
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Dihydroartemisinin-Piperaquine for the Prevention of Malaria in Pregnancy
NEW ENGLAND JOURNAL OF MEDICINE
Kakuru, A., Jagannathan, P., Muhindo, M. K., Natureeba, P., Awori, P., Nakalembe, M., Opira, B., Olwoch, P., Ategeka, J., Nayebare, P., Clark, T. D., Feeney, M. E., Charlebois, E. D., Rizzuto, G., Muehlenbachs, A., Havlir, D. V., Kamya, M. R., Dorsey, G.
2016; 374 (10): 928-939
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Abstract
Intermittent treatment with sulfadoxine-pyrimethamine is widely recommended for the prevention of malaria in pregnant women in Africa. However, with the spread of resistance to sulfadoxine-pyrimethamine, new interventions are needed.We conducted a double-blind, randomized, controlled trial involving 300 human immunodeficiency virus (HIV)-uninfected pregnant adolescents or women in Uganda, where sulfadoxine-pyrimethamine resistance is widespread. We randomly assigned participants to a sulfadoxine-pyrimethamine regimen (106 participants), a three-dose dihydroartemisinin-piperaquine regimen (94 participants), or a monthly dihydroartemisinin-piperaquine regimen (100 participants). The primary outcome was the prevalence of histopathologically confirmed placental malaria.The prevalence of histopathologically confirmed placental malaria was significantly higher in the sulfadoxine-pyrimethamine group (50.0%) than in the three-dose dihydroartemisinin-piperaquine group (34.1%, P=0.03) or the monthly dihydroartemisinin-piperaquine group (27.1%, P=0.001). The prevalence of a composite adverse birth outcome was lower in the monthly dihydroartemisinin-piperaquine group (9.2%) than in the sulfadoxine-pyrimethamine group (18.6%, P=0.05) or the three-dose dihydroartemisinin-piperaquine group (21.3%, P=0.02). During pregnancy, the incidence of symptomatic malaria was significantly higher in the sulfadoxine-pyrimethamine group (41 episodes over 43.0 person-years at risk) than in the three-dose dihydroartemisinin-piperaquine group (12 episodes over 38.2 person-years at risk, P=0.001) or the monthly dihydroartemisinin-piperaquine group (0 episodes over 42.3 person-years at risk, P<0.001), as was the prevalence of parasitemia (40.5% in the sulfadoxine-pyrimethamine group vs. 16.6% in the three-dose dihydroartemisinin-piperaquine group [P<0.001] and 5.2% in the monthly dihydroartemisinin-piperaquine group [P<0.001]). In each treatment group, the risk of vomiting after administration of any dose of the study agents was less than 0.4%, and there were no significant differences among the groups in the risk of adverse events.The burden of malaria in pregnancy was significantly lower among adolescent girls or women who received intermittent preventive treatment with dihydroartemisinin-piperaquine than among those who received sulfadoxine-pyrimethamine, and monthly treatment with dihydroartemisinin-piperaquine was superior to three-dose dihydroartemisinin-piperaquine with regard to several outcomes. (Funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development; ClinicalTrials.gov number, NCT02163447.).
View details for DOI 10.1056/NEJMoa1509150
View details for Web of Science ID 000371660000006
View details for PubMedID 26962728
The Parsonnet Lab
Investigating Chronic Disease-Infection Links
The laboratory's primary research interest is investigating the role of infectious agents in chronic diseases. Much of this work has revolved around Helicobacter pylori infection as a cause of adenocarcinomas and lymphomas of the stomach.
Publications
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Decreasing human body temperature in the United States since the industrial revolution.
eLife
Protsiv, M., Ley, C., Lankester, J., Hastie, T., Parsonnet, J.
2020; 9
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Abstract
In the US, the normal, oral temperature of adults is, on average, lower than the canonical 37°C established in the 19th century. We postulated that body temperature has decreased over time. Using measurements from three cohorts--the Union Army Veterans of the Civil War (N = 23,710; measurement years 1860-1940), the National Health and Nutrition Examination Survey I (N = 15,301; 1971-1975), and the Stanford Translational Research Integrated Database Environment (N = 150,280; 2007-2017)--we determined that mean body temperature in men and women, after adjusting for age, height, weight and, in some models date and time of day, has decreased monotonically by 0.03°C per birth decade. A similar decline within the Union Army cohort as between cohorts, makes measurement error an unlikely explanation. This substantive and continuing shift in body temperature-a marker for metabolic rate-provides a framework for understanding changes in human health and longevity over 157 years.
View details for DOI 10.7554/eLife.49555
View details for PubMedID 31908267
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Prevalence of SARS-CoV-2 antibodies in a large nationwide sample of patients on dialysis in the USA: a cross-sectional study.
Lancet (London, England)
Anand, S., Montez-Rath, M., Han, J., Bozeman, J., Kerschmann, R., Beyer, P., Parsonnet, J., Chertow, G. M.
2020
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Abstract
Many patients receiving dialysis in the USA share the socioeconomic characteristics of underserved communities, and undergo routine monthly laboratory testing, facilitating a practical, unbiased, and repeatable assessment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seroprevalence.For this cross-sectional study, in partnership with a central laboratory that receives samples from approximately 1300 dialysis facilities across the USA, we tested the remainder plasma of 28 503 randomly selected adult patients receiving dialysis in July, 2020, using a spike protein receptor binding domain total antibody chemiluminescence assay (100% sensitivity, 99·8% specificity). We extracted data on age, sex, race and ethnicity, and residence and facility ZIP codes from the anonymised electronic health records, linking patient-level residence data with cumulative and daily cases and deaths per 100 000 population and with nasal swab test positivity rates. We standardised prevalence estimates according to the overall US dialysis and adult population, and present estimates for four prespecified strata (age, sex, region, and race and ethnicity).The sampled population had similar age, sex, and race and ethnicity distribution to the US dialysis population, with a higher proportion of older people, men, and people living in majority Black and Hispanic neighbourhoods than in the US adult population. Seroprevalence of SARS-CoV-2 was 8·0% (95% CI 7·7-8·4) in the sample, 8·3% (8·0-8·6) when standardised to the US dialysis population, and 9·3% (8·8-9·9) when standardised to the US adult population. When standardised to the US dialysis population, seroprevalence ranged from 3·5% (3·1-3·9) in the west to 27·2% (25·9-28·5) in the northeast. Comparing seroprevalent and case counts per 100 000 population, we found that 9·2% (8·7-9·8) of seropositive patients were diagnosed. When compared with other measures of SARS-CoV-2 spread, seroprevalence correlated best with deaths per 100 000 population (Spearman's ρ=0·77). Residents of non-Hispanic Black and Hispanic neighbourhoods experienced higher odds of seropositivity (odds ratio 3·9 [95% CI 3·4-4·6] and 2·3 [1·9-2·6], respectively) compared with residents of predominantly non-Hispanic white neighbourhoods. Residents of neighbourhoods in the highest population density quintile experienced increased odds of seropositivity (10·3 [8·7-12·2]) compared with residents of the lowest density quintile. County mobility restrictions that reduced workplace visits by at least 5% in early March, 2020, were associated with lower odds of seropositivity in July, 2020 (0·4 [0·3-0·5]) when compared with a reduction of less than 5%.During the first wave of the COVID-19 pandemic, fewer than 10% of the US adult population formed antibodies against SARS-CoV-2, and fewer than 10% of those with antibodies were diagnosed. Public health efforts to limit SARS-CoV-2 spread need to especially target racial and ethnic minority and densely populated communities.Ascend Clinical Laboratories.
View details for DOI 10.1016/S0140-6736(20)32009-2
View details for PubMedID 32987007
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Shaping of infant B cell receptor repertoires by environmental factors and infectious disease.
Science translational medicine
Nielsen, S. C., Roskin, K. M., Jackson, K. J., Joshi, S. A., Nejad, P., Lee, J., Wagar, L. E., Pham, T. D., Hoh, R. A., Nguyen, K. D., Tsunemoto, H. Y., Patel, S. B., Tibshirani, R., Ley, C., Davis, M. M., Parsonnet, J., Boyd, S. D.
2019; 11 (481)
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Antigenic exposures at epithelial sites in infancy and early childhood are thought to influence the maturation of humoral immunity and modulate the risk of developing immunoglobulin E (IgE)-mediated allergic disease. How different kinds of environmental exposures influence B cell isotype switching to IgE, IgG, or IgA, and the somatic mutation maturation of these antibody pools, is not fully understood. We sequenced antibody repertoires in longitudinal blood samples in a birth cohort from infancy through the first 3 years of life and found that, whereas IgG and IgA show linear increases in mutational maturation with age, IgM and IgD mutations are more closely tied to pathogen exposure. IgE mutation frequencies are primarily increased in children with impaired skin barrier conditions such as eczema, suggesting that IgE affinity maturation could provide a mechanistic link between epithelial barrier failure and allergy development.
View details for PubMedID 30814336
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Increased T Cell Differentiation and Cytolytic Function in Bangladeshi Compared to American Children.
Frontiers in immunology
Wagar, L. E., Bolen, C. R., Sigal, N., Lopez Angel, C. J., Guan, L., Kirkpatrick, B. D., Haque, R., Tibshirani, R. J., Parsonnet, J., Petri, W. A., Davis, M. M.
2019; 10: 2239
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During the first 5 years of life, children are especially vulnerable to infection-related morbidity and mortality. Conversely, the Hygiene Hypothesis suggests that a lack of exposure to infectious agents early in life could explain the increasing incidence of allergies and autoimmunity in high-income countries. Understanding these phenomena, however, is hampered by a lack of comprehensive, direct immune monitoring in children with differing degrees of microbial exposure. Using mass cytometry, we provide an in-depth profile of the peripheral blood mononuclear cells (PBMCs) of children in regions at the extremes of exposure: the San Francisco Bay Area, USA and an economically poor district of Dhaka, Bangladesh. Despite variability in clinical health, functional characteristics of PBMCs were similar in Bangladeshi and American children at 1 year of age. However, by 2-3 years of age, Bangladeshi children's immune cells often demonstrated altered activation and cytokine production profiles upon stimulation with PMA-ionomycin, with an overall immune trajectory more in line with American adults. Conversely, immune responses in children from the US remained steady. Using principal component analysis, donor location, ethnic background, and cytomegalovirus infection status were found to account for some of the variation identified among samples. Within Bangladeshi 1-year-olds, stunting (as measured by height-for-age z-scores) was found to be associated with IL-8 and TGFβ expression in PMA-ionomycin stimulated samples. Combined, these findings provide important insights into the immune systems of children in high vs. low microbial exposure environments and suggest an important role for IL-8 and TGFβ in mitigating the microbial challenges faced by the Bangladeshi children.
View details for DOI 10.3389/fimmu.2019.02239
View details for PubMedID 31620139
View details for PubMedCentralID PMC6763580
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Time for Helicobacter pylori eradication.
The Lancet. Infectious diseases
Parsonnet, J.
2019; 19 (10): 1042–43
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View details for DOI 10.1016/S1473-3099(19)30406-2
View details for PubMedID 31559950
The Relman Lab
Host-Microbe Interactions & Human Microbial Ecology
David Relman's investigative program falls within the general themes of host-pathogen interactions and human microbial ecology, and is divided into two research areas:
- Ecology of microbial communities indigenous to humans and other mammalian hosts
- Genome-wide host response patterns in systemic infectious disease
Publications
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Microbiota assembly, structure, and dynamics among Tsimane horticulturalists of the Bolivian Amazon.
Nature communications
Sprockett, D. D., Martin, M., Costello, E. K., Burns, A. R., Holmes, S. P., Gurven, M. D., Relman, D. A.
2020; 11 (1): 3772
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Abstract
Selective and neutral forces shape human microbiota assembly in early life. The Tsimane are an indigenous Bolivian population with infant care-associated behaviors predicted to increase mother-infant microbial dispersal. Here, we characterize microbial community assembly in 47 infant-mother pairs from six Tsimane villages, using 16S rRNA gene amplicon sequencing of longitudinal stool and tongue swab samples. We find that infant consumption of dairy products, vegetables, and chicha (a fermented drink inoculated with oral microbes) is associated with stool microbiota composition. In stool and tongue samples, microbes shared between mothers and infants are more abundant than non-shared microbes. Using a neutral model of community assembly, we find that neutral processes alone explain the prevalence of 79% of infant-colonizing microbes, but explain microbial prevalence less well in adults from river villages with more regular access to markets. Our results underscore the importance of neutral forces during microbiota assembly. Changing lifestyle factors may alter traditional modes of microbiota assembly by decreasing the role of neutral processes.
View details for DOI 10.1038/s41467-020-17541-6
View details for PubMedID 32728114
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Towards personalized medicine in maternal and child health: integrating biologic and social determinants.
Pediatric research
Stevenson, D. K., Wong, R. J., Aghaeepour, N., Maric, I., Angst, M. S., Contrepois, K., Darmstadt, G. L., Druzin, M. L., Eisenberg, M. L., Gaudilliere, B., Gibbs, R. S., Gotlib, I. H., Gould, J. B., Lee, H. C., Ling, X. B., Mayo, J. A., Moufarrej, M. N., Quaintance, C. C., Quake, S. R., Relman, D. A., Sirota, M., Snyder, M. P., Sylvester, K. G., Hao, S., Wise, P. H., Shaw, G. M., Katz, M.
2020
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View details for DOI 10.1038/s41390-020-0981-8
View details for PubMedID 32454518
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Unraveling the Role of the Gut Microbiome in Iron-Deficiency Anemia During Pregnancy
Celis, A., Relman, D.
WILEY. 2020
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View details for DOI 10.1096/fasebj.2020.34.s1.07369
View details for Web of Science ID 000546023103051
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Thinking about the microbiome as a causal factor in human health and disease: philosophical and experimental considerations.
Current opinion in microbiology
Relman, D. A.
2020; 54: 119–26
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Abstract
Relationships between hosts and host-associated microbial communities are complex, intimate, and associated with a wide variety of health and disease states. For these reasons, these relationships have raised many difficult questions and claims about microbiome causation. While philosophers and scientists alike have pondered the challenges of causal inference and offered postulates and rules, there are no simple solutions, especially with poorly characterized, putative causal factors such as microbiomes, ill-defined host effects, and inadequate experimental models. Recommendations are provided here for conceptual and experimental approaches regarding microbiome causal inference, and for a research agenda.
View details for DOI 10.1016/j.mib.2020.01.018
View details for PubMedID 32114367
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Clades of huge phages from across Earth's ecosystems.
Nature
Al-Shayeb, B., Sachdeva, R., Chen, L., Ward, F., Munk, P., Devoto, A., Castelle, C. J., Olm, M. R., Bouma-Gregson, K., Amano, Y., He, C., Meheust, R., Brooks, B., Thomas, A., Lavy, A., Matheus-Carnevali, P., Sun, C., Goltsman, D. S., Borton, M. A., Sharrar, A., Jaffe, A. L., Nelson, T. C., Kantor, R., Keren, R., Lane, K. R., Farag, I. F., Lei, S., Finstad, K., Amundson, R., Anantharaman, K., Zhou, J., Probst, A. J., Power, M. E., Tringe, S. G., Li, W., Wrighton, K., Harrison, S., Morowitz, M., Relman, D. A., Doudna, J. A., Lehours, A., Warren, L., Cate, J. H., Santini, J. M., Banfield, J. F.
2020
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Abstract
Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200kilobases (kb), including a genome of 735kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.
View details for DOI 10.1038/s41586-020-2007-4
View details for PubMedID 32051592
The Shafer Lab
Virus Evolution focused on HIV Therapy and Drug Resistance
My group’s research is on the mechanisms and consequences of virus evolution with a focus on HIV therapy and drug resistance. We maintain a public HIV drug resistance database (http://hivdb.stanford.edu) as a resource for HIV drug resistance surveillance, interpreting HIV drug resistance tests, and HIV drug development. These three disciplines – epidemiology, clinical management, and basic science – reflect the interdisciplinary nature of antiviral drug resistance research and represent the range of our group’s activities.
Publications
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Virological Failure and Acquired Genotypic Resistance Associated With Contemporary Antiretroviral Treatment Regimens.
Open forum infectious diseases
Rhee, S. Y., Clutter, D., Hare, C. B., Tchakoute, C. T., Sainani, K., Fessel, W. J., Hurley, L., Slome, S., Pinsky, B. A., Silverberg, M. J., Shafer, R. W.
2020; 7 (9): ofaa316
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Abstract
There are few descriptions of virologic failure (VF) and acquired drug resistance (HIVDR) in large cohorts initiating contemporary antiretroviral therapy (ART).We studied all persons with HIV (PWH) in a California clinic population initiating ART between 2010 and 2017. VF was defined as not attaining virologic suppression, discontinuing ART, or virologic rebound prompting change in ART.During the study, 2315 PWH began ART. Six companion drugs were used in 93.3% of regimens: efavirenz, elvitegravir/c, dolutegravir, b-darunavir, rilpivirine, and raltegravir. During a median follow-up of 36 months, 214 (9.2%) PWH experienced VF (2.8 per 100 person-years) and 62 (2.7%) experienced HIVDR (0.8 per 100 person-years). In multivariable analyses, younger age, lower CD4 count, higher virus load, and b-atazanavir were associated with increased VF risk; lower CD4 count, higher virus load, and nevirapine were associated with increased HIVDR risk. Compared with efavirenz, dolutegravir, raltegravir, and b-darunavir were associated with reduced HIVDR risk. Risks of VF and HIVDR were not significantly associated with ART initiation year. Of the 62 PWH with HIVDR, 42 received an non-nucleoside RT inhibitor (NNRTI), 15 an integrase-strand transfer inhibitor (INSTI), and 5 a protease inhibitor (PI). Among those with HIVDR on an NNRTI or first-generation INSTI, 59% acquired dual class resistance and 29% developed tenofovir resistance; those receiving a PI or dolutegravir developed just M184V.Despite the frequent use of contemporary ART regimens, VF and HIVDR continue to occur. Further efforts are required to improve long-term ART virological responses to prevent the consequences of ongoing HIV-1 replication including virus transmission and HIVDR.
View details for DOI 10.1093/ofid/ofaa316
View details for PubMedID 32904894
View details for PubMedCentralID PMC7462367
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Analysis of unusual and signature APOBEC-mutations in HIV-1 pol next-generation sequences.
PloS one
Tzou, P. L., Kosakovsky Pond, S. L., Avila-Rios, S., Holmes, S. P., Kantor, R., Shafer, R. W.
2020; 15 (2): e0225352
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Abstract
At low mutation-detection thresholds, next generation sequencing (NGS) for HIV-1 genotypic resistance testing is susceptible to artifactual detection of mutations arising from PCR error and APOBEC-mediated G-to-A hypermutation.We analyzed published HIV-1 pol Illumina NGS data to characterize the distribution of mutations at eight NGS mutation detection thresholds: 20%, 10%, 5%, 2%, 1%, 0.5%, 0.2%, and 0.1%. At each threshold, we determined proportions of amino acid mutations that were unusual (defined as having a prevalence <0.01% in HIV-1 group M sequences) or signature APOBEC mutations.Eight studies, containing 855 samples, in the NCBI Sequence Read Archive were analyzed. As detection thresholds were lowered, there was a progressive increase in the proportion of positions with usual and unusual mutations and in the proportion of all mutations that were unusual. The median proportion of positions with an unusual mutation increased gradually from 0% at the 20% threshold to 0.3% at the 1% threshold and then exponentially to 1.3% (0.5% threshold), 6.9% (0.2% threshold), and 23.2% (0.1% threshold). In two of three studies with available plasma HIV-1 RNA levels, the proportion of positions with unusual mutations was negatively associated with virus levels. Although the complete set of signature APOBEC mutations was much smaller than that of unusual mutations, the former outnumbered the latter in one-sixth of samples at the 0.5%, 1%, and 2% thresholds.The marked increase in the proportion of positions with unusual mutations at thresholds below 1% and in samples with lower virus loads suggests that, at low thresholds, many unusual mutations are artifactual, reflecting PCR error or G-to-A hypermutation. Profiling the numbers of unusual and signature APOBEC pol mutations at different NGS mutation detection thresholds may be useful to avoid selecting a threshold that is too low and poses an unacceptable risk of identifying artifactual mutations.
View details for DOI 10.1371/journal.pone.0225352
View details for PubMedID 32102090
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Coronavirus Antiviral Research Database (CoV-RDB): An Online Database Designed to Facilitate Comparisons between Candidate Anti-Coronavirus Compounds.
Viruses
Tzou, P. L., Tao, K., Nouhin, J., Rhee, S. Y., Hu, B. D., Pai, S., Parkin, N., Shafer, R. W.
2020; 12 (9)
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Abstract
To prioritize the development of antiviral compounds, it is necessary to compare their relative preclinical activity and clinical efficacy.We reviewed in vitro, animal model, and clinical studies of candidate anti-coronavirus compounds and placed extracted data in an online relational database.As of August 2020, the Coronavirus Antiviral Research Database (CoV-RDB; covdb.stanford.edu) contained over 2800 cell culture, entry assay, and biochemical experiments, 259 animal model studies, and 73 clinical studies from over 400 published papers. SARS-CoV-2, SARS-CoV, and MERS-CoV account for 85% of the data. Approximately 75% of experiments involved compounds with known or likely mechanisms of action, including monoclonal antibodies and receptor binding inhibitors (21%), viral protease inhibitors (17%), miscellaneous host-acting inhibitors (10%), polymerase inhibitors (9%), interferons (7%), fusion inhibitors (5%), and host protease inhibitors (5%). Of 975 compounds with known or likely mechanism, 135 (14%) are licensed in the U.S. for other indications, 197 (20%) are licensed outside the U.S. or are in human trials, and 595 (61%) are pre-clinical investigational compounds.CoV-RDB facilitates comparisons between different candidate antiviral compounds, thereby helping scientists, clinical investigators, public health officials, and funding agencies prioritize the most promising compounds and repurposed drugs for further development.
View details for DOI 10.3390/v12091006
View details for PubMedID 32916958
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Multiplex Solid-Phase Melt Curve Analysis for the Point-of-Care Detection of HIV-1 Drug Resistance
JOURNAL OF MOLECULAR DIAGNOSTICS
Clutter, D. S., Mazarei, G., Sinha, R., Manasa, J., Nouhin, J., LaPrade, E., Bolouki, S., Tzou, P. L., Hannita-Hui, J., Sahoo, M. K., Kuimelis, P., Kuimelis, R. G., Pinsky, B. A., Schoolnik, G. K., Hassibi, A., Shafer, R. W.
2019; 21 (4): 580–92
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View details for DOI 10.1016/j.jmoldx.2019.02.005
View details for Web of Science ID 000475412100005
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Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted Human Immunodeficiency Virus Type 1 Drug Resistance in a Large US Clinic Population
CLINICAL INFECTIOUS DISEASES
Rhee, S., Clutter, D., Fessel, W., Klein, D., Slome, S., Pinsky, B. A., Marcus, J. L., Hurley, L., Silverberg, M. J., Pond, S., Shafer, R. W.
2019; 68 (2): 213–21
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View details for DOI 10.1093/cid/ciy453
View details for Web of Science ID 000459636700010
The Singh Lab
Identifying Virulence Mechanisms Parasites Develop to Cause Disease
Our lab studies the molecular basis of pathogenesis of two medically important parasites, Toxoplasma gondii and Entamoeba histolytica. The work is aimed at understanding the virulence determinant that each parasite uses in causing disease, specifically how T. gondii evades the human immune response by converting to a dormant bradyzoite stage and how E. histolyticacauses invasive colonic and hepatic disease.
Publications
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Identification of anisomycin, prodigiosin and obatoclax as compounds with broad-spectrum anti-parasitic activity
PLOS NEGLECTED TROPICAL DISEASES
Ehrenkaufer, G., Li, P., Stebbins, E. E., Kangussu-Marcolino, M. M., Debnath, A., White, C., Moser, M. S., DeRisi, J., Gisselberg, J., Yeh, E., Wang, S. C., Company, A., Monti, L., Caffrey, C. R., Huston, C. D., Wang, B., Singh, U.
2020; 14 (3)
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View details for DOI 10.1371/journal.pntd.0008150.r004
View details for Web of Science ID 000528655400050
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Entamoeba stage conversion: progress and new insights.
Current opinion in microbiology
Manna, D., Ehrenkaufer, G. M., Lozano-Amado, D., Singh, U.
2020; 58: 62–68
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Abstract
Entamoeba histolytica, an anaerobic protozoan, is an important global health problem. This parasite has a biphasic life cycle consisting of a dormant cyst stage which is environmentally resistant and transmits the infection, and the proliferative trophozoite stage which is motile and causes invasive disease. The stage conversion process remains poorly understood despite being central to amoebic biology. In this review, we will highlight recent progress in our understanding of Entamoeba stage conversion including dissecting transcriptome analysis in development, characterization of transcriptional networks, demonstration of epigenetic regulation, and role of small molecules that regulate Entamoeba development.
View details for DOI 10.1016/j.mib.2020.09.005
View details for PubMedID 33032142
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The NAD+ Responsive Transcription Factor ERM-BP Functions Downstream of Cellular Aggregation and Is an Early Regulator of Development and Heat Shock Response in Entamoeba.
Frontiers in cellular and infection microbiology
Manna, D., Lozano-Amado, D., Ehrenkaufer, G., Singh, U.
2020; 10: 363
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Abstract
Entamoeba histolytica is a protozoan parasite and a major cause of dysentery and diarrheal disease in developing countries. Disease transmission from one host to another occurs via cysts which can survive in environmental extremes and are transmitted through contaminated food and water. Recent studies in our lab identified a novel transcription factor, Encystation Regulatory Motif- Binding Protein (ERM-BP), which is responsive to NAD+ and has an important role in encystation. The key residues important for ERM-BP function were demonstrated in vitro using recombinant protein. In this study we demonstrate the in vivo functional consequences of mutations in key domains and their impact on Entamoeba encystation. Our results show that mutations in the DNA binding domain (ERM-BP-DBM) and in the nicotinamidase domain (ERM-BP-C198A) lead to protein mis-localization in both trophozoites and cysts and significantly reduce encystation efficiency. Additionally, we showed that silencing of ERM-BP significantly decreased the size and number of multi-nucleated giant cells (MGC) that form during encystation, indicating that ERM-BP functions upstream of the cellular aggregation that precedes stage conversion. Dissection of epistatic interactions between ERM-BP and a second encystation-related transcription factor, NF-Y revealed that ERM-BP is upstream of NF-Y in controlling the developmental cascade and appears to be one of the earliest regulators of development identified to date in Entamoeba. We also demonstrated that ERM-BP is upregulated during heat stress in Entamoeba, another condition which increases intracellular NAD+ levels and that overexpression of ERM-BP makes E. histolytica and E. invadens parasites more resistant to heat stress. Overexpression of ERM-BP in E. histolytica also induced the formation of cyst-like quadrinucleated cells and formation of MGCs. Overall, our work has identified an important role of ERM-BP in Entamoeba stress response and links an NAD+-responsive transcription factor to both development and heat shock response. Characterization of stress and developmental cascades are important avenues to investigate for Entamoeba, an important human parasitic pathogen.
View details for DOI 10.3389/fcimb.2020.00363
View details for PubMedID 32766170
View details for PubMedCentralID PMC7379229
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Interferon-gamma release assay for accurate detection of SARS-CoV-2 T cell response.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
Murugesan, K., Jagannathan, P., Pham, T. D., Pandey, S., Bonilla, H. F., Jacobson, K., Parsonnet, J., Andrews, J. R., Weiskopf, D., Sette, A., Pinsky, B. A., Singh, U., Banaei, N.
2020
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Abstract
We investigated feasibility and accuracy of an interferon-gamma release assay (IGRA) for detection of T cell responses to SARS-CoV-2. Whole blood IGRA accurately distinguished between convalescents and uninfected healthy blood donors with a predominantly CD4+ T cell response. SARS-CoV-2 IGRA may serve as a useful diagnostic tool in managing the COVID-19 pandemic.
View details for DOI 10.1093/cid/ciaa1537
View details for PubMedID 33035306
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Proinflammatory IgG Fc structures in patients with severe COVID-19
Nature Immunology
Chakraborty, S.
2020
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View details for DOI 10.1038/s41590-020-00828-7
The Wang Lab
Human Immune Functions & Susceptibility to Diseases
Taia Wang’s laboratory studies mechanisms underlying the heterogeneity in human immune function during vaccination and viral infection. We are particularly interested in antibody-mediated immunity and determinants of susceptibility to antibody-mediated diseases.
Publications
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Immunoglobulin E sialylation regulates allergic responses.
Immunology and cell biology
Xie, M. M., Bertozzi, C. R., Wang, T. T.
2020
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Abstract
Shade et al. demonstrate that people with peanut allergies produce IgE antibodies that are enriched for sialic acid-containing glycoforms. The sialylated IgE triggered significantly more degranulation by basophils and mast cells, suggesting intrinsic functional differences between IgEs from allergic and nonallergic subjects.
View details for DOI 10.1111/imcb.12368
View details for PubMedID 32632971
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Maternal Anti-Dengue IgG Fucosylation Predicts Susceptibility to Dengue Disease in Infants.
Cell reports
Thulin, N. K., Brewer, R. C., Sherwood, R., Bournazos, S., Edwards, K. G., Ramadoss, N. S., Taubenberger, J. K., Memoli, M., Gentles, A. J., Jagannathan, P., Zhang, S., Libraty, D. H., Wang, T. T.
2020; 31 (6): 107642
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Abstract
Infant mortality from dengue disease is a devastating global health burden that could be minimized with the ability to identify susceptibility for severe disease prior to infection. Although most primary infant dengue infections are asymptomatic, maternally derived anti-dengue immunoglobulin G (IgGs) present during infection can trigger progression to severe disease through antibody-dependent enhancement mechanisms. Importantly, specific characteristics of maternal IgGs that herald progression to severe infant dengue are unknown. Here, we define ≥10% afucosylation of maternal anti-dengue IgGs as a risk factor for susceptibility of infants to symptomatic dengue infections. Mechanistic experiments show that afucosylation of anti-dengue IgGs promotes FcgammaRIIIa signaling during infection, in turn enhancing dengue virus replication in FcgammaRIIIa+ monocytes. These studies identify a post-translational modification of anti-dengue IgGs that correlates with risk for symptomatic infant dengue infections and define a mechanism by which afucosylated antibodies and FcgammaRIIIa enhance dengue infections.
View details for DOI 10.1016/j.celrep.2020.107642
View details for PubMedID 32402275
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Proinflammatory IgG Fc structures in patients with severe COVID-19
Nature Immunology
Chakraborty, S.
2020
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View details for DOI 10.1038/s41590-020-00828-7
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FcRn, but not FcγRs, drives maternal-fetal transplacental transport of human IgG antibodies.
Proceedings of the National Academy of Sciences of the United States of America
Borghi, S., Bournazos, S., Thulin, N. K., Li, C., Gajewski, A., Sherwood, R. W., Zhang, S., Harris, E., Jagannathan, P., Wang, L. X., Ravetch, J. V., Wang, T. T.
2020
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Abstract
The IgG Fc domain has the capacity to interact with diverse types of receptors, including the neonatal Fc receptor (FcRn) and Fcγ receptors (FcγRs), which confer pleiotropic biological activities. Whereas FcRn regulates IgG epithelial transport and recycling, Fc effector activities, such as antibody-dependent cellular cytotoxicity (ADCC) and phagocytosis, are mediated by FcγRs, which upon cross-linking transduce signals that modulate the function of effector leukocytes. Despite the well-defined and nonoverlapping functional properties of FcRn and FcγRs, recent studies have suggested that FcγRs mediate transplacental IgG transport, as certain Fc glycoforms were reported to be enriched in fetal circulation. To determine the contribution of FcγRs and FcRn to the maternal-fetal transport of IgG, we characterized the IgG Fc glycosylation in paired maternal-fetal samples from patient cohorts from Uganda and Nicaragua. No differences in IgG1 Fc glycan profiles and minimal differences in IgG2 Fc glycans were noted, whereas the presence or absence of galactose on the Fc glycan of IgG1 did not alter FcγRIIIa or FcRn binding, half-life, or their ability to deplete target cells in FcγR/FcRn humanized mice. Modeling maternal-fetal transport in FcγR/FcRn humanized mice confirmed that only FcRn contributed to transplacental transport of IgG; IgG selectively enhanced for FcRn binding resulted in enhanced accumulation of maternal antibody in the fetus. In contrast, enhancing FcγRIIIa binding did not result in enhanced maternal-fetal transport. These results argue against a role for FcγRs in IgG transplacental transport, suggesting Fc engineering of maternally administered antibody to enhance only FcRn binding as a means to improve maternal-fetal transport of IgG.
View details for DOI 10.1073/pnas.2004325117
View details for PubMedID 32461366
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Symptomatic SARS-CoV-2 infections display specific IgG Fc structures.
medRxiv : the preprint server for health sciences
Chakraborty, S., Edwards, K., Buzzanco, A. S., Memoli, M. J., Sherwood, R., Mallajosyula, V., Xie, M. M., Gonzalez, J., Buffone, C., Kathale, N., Providenza, S., Jagannathan, P., Andrews, J. R., Blish, C. A., Krammer, F., Dugan, H., Wilson, P. C., Pham, T. D., Boyd, S. D., Zhang, S., Taubenberger, J. K., Morales, T., Schapiro, J. M., Parsonnet, J., Wang, T. T.
2020
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Abstract
The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has caused a public health crisis that is exacerbated by our poor understanding of correlates of immunity. SARS-CoV-2 infection can cause Coronavirus Disease 2019 (COVID-19), with a spectrum of symptoms ranging from asymptomatic carriage to life threatening pneumonia and cytokine dysregulation [1-3]. Although antibodies have been shown in a variety of in vitro assays to promote coronavirus infections through mechanisms requiring interactions between IgG antibodies and Fc gamma receptors (FcγRs), the relevance of these observations to coronavirus infections in humans is not known [4-7]. In light of ongoing clinical trials examining convalescent serum therapy for COVID-19 patients and expedited SARS-CoV-2 vaccine testing in humans, it is essential to clarify the role of antibodies in the pathogenesis of COVID-19. Here we show that adults with PCR-diagnosed COVID-19 produce IgG antibodies with a specific Fc domain repertoire that is characterized by reduced fucosylation, a modification that enhances interactions with the activating FcγR, FcγRIIIa. Fc fucosylation was reduced when compared with SARS-CoV-2-seropositive children and relative to adults with symptomatic influenza virus infections. These results demonstrate an antibody correlate of symptomatic SARS-CoV-2 infections in adults and have implications for novel therapeutic strategies targeting FcγRIIIa pathways.
View details for DOI 10.1101/2020.05.15.20103341
View details for PubMedID 32511463
View details for PubMedCentralID PMC7252581