Publications by authors named "Lindsay Droit"

25 Publications

  • Page 1 of 1

A potently neutralizing anti-SARS-CoV-2 antibody inhibits variants of concern by binding a highly conserved epitope.

bioRxiv 2021 Apr 26. Epub 2021 Apr 26.

With the emergence of SARS-CoV-2 variants with increased transmissibility and potential resistance, antibodies and vaccines with broadly inhibitory activity are needed. Here we developed a panel of neutralizing anti-SARS-CoV-2 mAbs that bind the receptor binding domain of the spike protein at distinct epitopes and block virus attachment to cells and its receptor, human angiotensin converting enzyme-2 (hACE2). While several potently neutralizing mAbs protected K18-hACE2 transgenic mice against infection caused by historical SARS-CoV-2 strains, others induced escape variants in vivo and lost activity against emerging strains. We identified one mAb, SARS2-38, that potently neutralizes all SARS-CoV-2 variants of concern tested and protects mice against challenge by multiple SARS-CoV-2 strains. Structural analysis showed that SARS2-38 engages a conserved epitope proximal to the receptor binding motif. Thus, treatment with or induction of inhibitory antibodies that bind conserved spike epitopes may limit the loss of potency of therapies or vaccines against emerging SARS-CoV-2 variants.
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http://dx.doi.org/10.1101/2021.04.26.441501DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8077627PMC
April 2021

SARS-CoV-2 E gene variant alters analytical sensitivity characteristics of viral detection using a commercial RT-PCR assay.

J Clin Microbiol 2021 Apr 26. Epub 2021 Apr 26.

Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO

Diagnostic assays for detecting SARS-CoV-2 are essential for patient management, infection prevention, and the public health response for COVID-19. The efficacy and reliability of these assays are of paramount importance in both tracking and controlling spread of the virus. Real-time RT-PCR assays rely on a fixed genetic sequence for primers and probe binding. Mutations can potentially alter the accuracy of these assays and lead to unpredictable analytical performance characteristics and false-negative results. Herein, we identify a G-to-U transversion (nucleotide 26372) in the SARS-CoV-2 E gene in three specimens with reduced viral detection efficiency using a widely available commercial assay. Further analysis of the public GISAID repository led to the identification of 18 additional genomes with this mutation, which reflect five independent mutational events. This work supports the use of dual-target assays to reduce the number of false-negative PCR results.
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http://dx.doi.org/10.1128/JCM.00075-21DOI Listing
April 2021

Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies.

Nat Med 2021 04 4;27(4):717-726. Epub 2021 Mar 4.

Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the global COVID-19 pandemic. Rapidly spreading SARS-CoV-2 variants may jeopardize newly introduced antibody and vaccine countermeasures. Here, using monoclonal antibodies (mAbs), animal immune sera, human convalescent sera and human sera from recipients of the BNT162b2 mRNA vaccine, we report the impact on antibody neutralization of a panel of authentic SARS-CoV-2 variants including a B.1.1.7 isolate, chimeric strains with South African or Brazilian spike genes and isogenic recombinant viral variants. Many highly neutralizing mAbs engaging the receptor-binding domain or N-terminal domain and most convalescent sera and mRNA vaccine-induced immune sera showed reduced inhibitory activity against viruses containing an E484K spike mutation. As antibodies binding to spike receptor-binding domain and N-terminal domain demonstrate diminished neutralization potency in vitro against some emerging variants, updated mAb cocktails targeting highly conserved regions, enhancement of mAb potency or adjustments to the spike sequences of vaccines may be needed to prevent loss of protection in vivo.
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http://dx.doi.org/10.1038/s41591-021-01294-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8058618PMC
April 2021

SARS-CoV-2 variants show resistance to neutralization by many monoclonal and serum-derived polyclonal antibodies.

Res Sq 2021 Feb 10. Epub 2021 Feb 10.

The University of Texas Medical Branch at Galveston.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the global COVID-19 pandemic infecting more than 106 million people and causing 2.3 million deaths. The rapid deployment of antibody-based countermeasures has provided hope for curtailing disease and ending the pandemic . However, the emergence of rapidly-spreading SARS-CoV-2 variants in the United Kingdom (B.1.1.7), South Africa (B.1.351), and elsewhere with mutations in the spike protein has raised concern for escape from neutralizing antibody responses and loss of vaccine efficacy based on preliminary data with pseudoviruses . Here, using monoclonal antibodies (mAbs), animal immune sera, human convalescent sera, and human sera from recipients of the Pfizer-BioNTech (BNT162b2) mRNA vaccine, we report the impact on antibody neutralization of a panel of authentic SARS-CoV-2 variants including a B.1.1.7 isolate, a chimeric Washington strain with a South African spike gene (Wash SA-B.1.351), and isogenic recombinant variants with designed mutations or deletions at positions 69-70, 417, 484, 501, and/or 614 of the spike protein. Several highly neutralizing mAbs engaging the receptor binding domain (RBD) or N-terminal domain (NTD) lost inhibitory activity against Wash SA-B.1.351 or recombinant variants with an E484K spike mutation. Most convalescent sera and virtually all mRNA vaccine-induced immune sera tested showed markedly diminished neutralizing activity against the Wash SA-B.1.351 strain or recombinant viruses containing mutations at position 484 and 501. We also noted that cell line selection used for growth of virus stocks or neutralization assays can impact the potency of antibodies against different SARS-CoV-2 variants, which has implications for assay standardization and congruence of results across laboratories. As several antibodies binding specific regions of the RBD and NTD show loss-of-neutralization potency against emerging variants, updated mAb cocktails, targeting of highly conserved regions, enhancement of mAb potency, or adjustments to the spike sequences of vaccines may be needed to prevent loss of protection .
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http://dx.doi.org/10.21203/rs.3.rs-228079/v1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7885928PMC
February 2021

UFMylation inhibits the proinflammatory capacity of interferon-γ-activated macrophages.

Proc Natl Acad Sci U S A 2021 01;118(1)

Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110;

Macrophages activated with interferon-γ (IFN-γ) in combination with other proinflammatory stimuli, such as lipopolysaccharide or tumor necrosis factor-α (TNF-α), respond with transcriptional and cellular changes that enhance clearance of intracellular pathogens at the risk of damaging tissues. IFN-γ effects must therefore be carefully balanced with inhibitory mechanisms to prevent immunopathology. We performed a genome-wide CRISPR knockout screen in a macrophage cell line to identify negative regulators of IFN-γ responses. We discovered an unexpected role of the ubiquitin-fold modifier (Ufm1) conjugation system (herein UFMylation) in inhibiting responses to IFN-γ and lipopolysaccharide. Enhanced IFN-γ activation in UFMylation-deficient cells resulted in increased transcriptional responses to IFN-γ in a manner dependent on endoplasmic reticulum stress responses involving Ern1 and Xbp1. Furthermore, UFMylation in myeloid cells is required for resistance to influenza infection in mice, indicating that this pathway modulates in vivo responses to infection. These findings provide a genetic roadmap for the regulation of responses to a key mediator of cellular immunity and identify a molecular link between the UFMylation pathway and immune responses.
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http://dx.doi.org/10.1073/pnas.2011763118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7817147PMC
January 2021

Neutralizing Antibody and Soluble ACE2 Inhibition of a Replication-Competent VSV-SARS-CoV-2 and a Clinical Isolate of SARS-CoV-2.

Cell Host Microbe 2020 09 3;28(3):475-485.e5. Epub 2020 Jul 3.

Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA. Electronic address:

Antibody-based interventions against SARS-CoV-2 could limit morbidity, mortality, and possibly transmission. An anticipated correlate of such countermeasures is the level of neutralizing antibodies against the SARS-CoV-2 spike protein, which engages with host ACE2 receptor for entry. Using an infectious molecular clone of vesicular stomatitis virus (VSV) expressing eGFP as a marker of infection, we replaced the glycoprotein gene (G) with the spike protein of SARS-CoV-2 (VSV-eGFP-SARS-CoV-2) and developed a high-throughput-imaging-based neutralization assay at biosafety level 2. We also developed a focus-reduction neutralization test with a clinical isolate of SARS-CoV-2 at biosafety level 3. Comparing the neutralizing activities of various antibodies and ACE2-Fc soluble decoy protein in both assays revealed a high degree of concordance. These assays will help define correlates of protection for antibody-based countermeasures and vaccines against SARS-CoV-2. Additionally, replication-competent VSV-eGFP-SARS-CoV-2 provides a tool for testing inhibitors of SARS-CoV-2 mediated entry under reduced biosafety containment.
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http://dx.doi.org/10.1016/j.chom.2020.06.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7332453PMC
September 2020

Neutralizing Antibody and Soluble ACE2 Inhibition of a Replication-Competent VSV-SARS-CoV-2 and a Clinical Isolate of SARS-CoV-2.

SSRN 2020 May 27:3606354. Epub 2020 May 27.

Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.

Antibody-based interventions against SARS-CoV-2 could limit morbidity, mortality, and possibly disrupt epidemic transmission. An anticipated correlate of such countermeasures is the level of neutralizing antibodies against the SARS-CoV-2 spike protein, yet there is no consensus as to which assay should be used for such measurements. Using an infectious molecular clone of vesicular stomatitis virus (VSV) that expresses eGFP as a marker of infection, we replaced the glycoprotein gene (G) with the spike protein of SARS-CoV-2 (VSV-eGFP-SARS-CoV-2) and developed a high-throughput imaging-based neutralization assay at biosafety level 2. We also developed a focus reduction neutralization test with a clinical isolate of SARS-CoV-2 at biosafety level 3. We compared the neutralizing activities of monoclonal and polyclonal antibody preparations, as well as ACE2-Fc soluble decoy protein in both assays and find an exceptionally high degree of concordance. The two assays will help define correlates of protection for antibody-based countermeasures including therapeutic antibodies, immune γ-globulin or plasma preparations, and vaccines against SARS-CoV-2. Replication-competent VSV-eGFP-SARS-CoV-2 provides a rapid assay for testing inhibitors of SARS-CoV-2 mediated entry that can be performed in 7.5 hours under reduced biosafety containment. Funding: This study was supported by NIH contracts and grants (75N93019C00062, HHSN272201700060C and R01 AI127828, R37 AI059371 and U01 AI151810) and the Defense Advanced Research Project Agency (HR001117S0019) and gifts from Washington University in Saint Louis. J.B.C. is supported by a Helen Hay Whitney Foundation postdoctoral fellowship. Conflict of Interest: M.S.D. is a consultant for Inbios, Vir Biotechnology, NGM Biopharmaceuticals, and on the Scientific Advisory Board of Moderna. D.C. and H.W.V. are employees of Vir Biotechnology Inc. and may hold shares in Vir Biotechnology Inc. S.P.J.W. and P.W.R. have filed a disclosure with Washington University for the recombinant VSV. Ethical Approval: This study was approved by the Mayo Clinic Institutional Review Board.
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http://dx.doi.org/10.2139/ssrn.3606354DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7366811PMC
May 2020

The Intestinal Microbiome Restricts Alphavirus Infection and Dissemination through a Bile Acid-Type I IFN Signaling Axis.

Cell 2020 08 14;182(4):901-918.e18. Epub 2020 Jul 14.

Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO 63110, USA. Electronic address:

Chikungunya virus (CHIKV), an emerging alphavirus, has infected millions of people. However, the factors modulating disease outcome remain poorly understood. Here, we show in germ-free mice or in oral antibiotic-treated conventionally housed mice with depleted intestinal microbiomes that greater CHIKV infection and spread occurs within 1 day of virus inoculation. Alteration of the microbiome alters TLR7-MyD88 signaling in plasmacytoid dendritic cells (pDCs) and blunts systemic production of type I interferon (IFN). Consequently, circulating monocytes express fewer IFN-stimulated genes and become permissive for CHIKV infection. Reconstitution with a single bacterial species, Clostridium scindens, or its derived metabolite, the secondary bile acid deoxycholic acid, can restore pDC- and MyD88-dependent type I IFN responses to restrict systemic CHIKV infection and transmission back to vector mosquitoes. Thus, symbiotic intestinal bacteria modulate antiviral immunity and levels of circulating alphaviruses within hours of infection through a bile acid-pDC-IFN signaling axis, which affects viremia, dissemination, and potentially transmission.
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http://dx.doi.org/10.1016/j.cell.2020.06.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7483520PMC
August 2020

Neutralizing antibody and soluble ACE2 inhibition of a replication-competent VSV-SARS-CoV-2 and a clinical isolate of SARS-CoV-2.

bioRxiv 2020 May 18. Epub 2020 May 18.

Antibody-based interventions against SARS-CoV-2 could limit morbidity, mortality, and possibly disrupt epidemic transmission. An anticipated correlate of such countermeasures is the level of neutralizing antibodies against the SARS-CoV-2 spike protein, yet there is no consensus as to which assay should be used for such measurements. Using an infectious molecular clone of vesicular stomatitis virus (VSV) that expresses eGFP as a marker of infection, we replaced the glycoprotein gene (G) with the spike protein of SARS-CoV-2 (VSV-eGFP-SARS-CoV-2) and developed a high-throughput imaging-based neutralization assay at biosafety level 2. We also developed a focus reduction neutralization test with a clinical isolate of SARS-CoV-2 at biosafety level 3. We compared the neutralizing activities of monoclonal and polyclonal antibody preparations, as well as ACE2-Fc soluble decoy protein in both assays and find an exceptionally high degree of concordance. The two assays will help define correlates of protection for antibody-based countermeasures including therapeutic antibodies, immune γ-globulin or plasma preparations, and vaccines against SARS-CoV-2. Replication-competent VSV-eGFP-SARS-CoV-2 provides a rapid assay for testing inhibitors of SARS-CoV-2 mediated entry that can be performed in 7.5 hours under reduced biosafety containment.
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http://dx.doi.org/10.1101/2020.05.18.102038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7263548PMC
May 2020

Select autophagy genes maintain quiescence of tissue-resident macrophages and increase susceptibility to Listeria monocytogenes.

Nat Microbiol 2020 02 20;5(2):272-281. Epub 2020 Jan 20.

Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.

Innate and adaptive immune responses that prime myeloid cells, such as macrophages, protect against pathogens. However, if left uncontrolled, these responses may lead to detrimental inflammation. Macrophages, particularly those resident in tissues, must therefore remain quiescent between infections despite chronic stimulation by commensal microorganisms. The genes required for quiescence of tissue-resident macrophages are not well understood. Autophagy, an evolutionarily conserved cellular process by which cytoplasmic contents are targeted for lysosomal digestion, has homeostatic functions including maintenance of protein and organelle integrity and regulation of metabolism. Recent research has shown that degradative autophagy, as well as various combinations of autophagy genes, regulate immunity and inflammation. Here, we delineate a function of the autophagy proteins Beclin 1 and FIP200-but not of other essential autophagy components ATG5, ATG16L1 or ATG7-in mediating quiescence of tissue-resident macrophages by limiting the effects of systemic interferon-γ. The perturbation of quiescence in mice that lack Beclin 1 or FIP200 in myeloid cells results in spontaneous immune activation and resistance to Listeria monocytogenes infection. While antibiotic-treated wild-type mice display diminished macrophage responses to inflammatory stimuli, this is not observed in mice that lack Beclin 1 in myeloid cells, establishing the dominance of this gene over effects of the bacterial microbiota. Thus, select autophagy genes, but not all genes essential for degradative autophagy, have a key function in maintaining immune quiescence of tissue-resident macrophages, resulting in genetically programmed susceptibility to bacterial infection.
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http://dx.doi.org/10.1038/s41564-019-0633-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147835PMC
February 2020

Virome biogeography in the lower gastrointestinal tract of rhesus macaques with chronic diarrhea.

Virology 2019 01 20;527:77-88. Epub 2018 Nov 20.

Departments of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA. Electronic address:

The composition of gastrointestinal tract viromes has been associated with multiple diseases. Our understanding of virus communities in the GI tract is still very limited due to challenges in sampling from different GI sites. Here we defined the GI viromes of 15 rhesus macaques with chronic diarrhea. Luminal content samples from terminal ileum, proximal and distal colon were collected at necropsy while samples from the rectum were collected antemortem using a fecal loop. The composition of and ecological parameters associated with the terminal ileum virome were distinct from the colon and rectum samples; these differences were driven by bacteriophages rather than eukaryotic viruses. The six contigs that were most discriminative of the viromes were distantly related to bacteriophages from three different families. Our analysis provides support for using fecal loop sampling of the rectum as a proxy of the colonic virome in humans.
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http://dx.doi.org/10.1016/j.virol.2018.10.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6333316PMC
January 2019

Effect of Antibiotic-Mediated Microbiome Modulation on Rotavirus Vaccine Immunogenicity: A Human, Randomized-Control Proof-of-Concept Trial.

Cell Host Microbe 2018 08;24(2):197-207.e4

Amsterdam UMC, University of Amsterdam, Department of Medicine, Division of Infectious Diseases and Center for Experimental and Molecular Medicine (CEMM), 1105 AZ, Amsterdam, the Netherlands.

Rotavirus vaccines (RVV) protect against childhood gastroenteritis caused by rotavirus (RV) but have decreased effectiveness in low- and middle-income settings. This proof-of-concept, randomized-controlled, open-label trial tested if microbiome modulation can improve RVV immunogenicity. Healthy adults were randomized and administered broad-spectrum (oral vancomycin, ciprofloxacin, metronidazole), narrow-spectrum (vancomycin), or no antibiotics and then vaccinated with RVV, 21 per group per protocol. Baseline anti-RV IgA was high in all subjects. Although antibiotics did not alter absolute anti-RV IgA titers, RVV immunogenicity was boosted at 7 days in the narrow-spectrum group. Further, antibiotics increased fecal shedding of RV while also rapidly altering gut bacterial beta diversity. Beta diversity associated with RVV immunogenicity boosting at day 7 and specific bacterial taxa that distinguish RVV boosters and RV shedders were identified. Despite the negative primary endpoint, this study demonstrates that microbiota modification alters the immune response to RVV and supports further exploration of microbiome manipulation to improve RVV immunogenicity.
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http://dx.doi.org/10.1016/j.chom.2018.07.005DOI Listing
August 2018

Alterations in the oral microbiome in HIV-infected participants after antiretroviral therapy administration are influenced by immune status.

AIDS 2018 06;32(10):1279-1287

University of Alabama, Birmingham, Alabama, USA.

Objective: To characterize the oral bacterial microbiome in HIV-infected participants at baseline and after 24 weeks of EFV/FTC/TDF.

Design: Thirty-five participants co-enrolled in two AIDS Clinical Trials Group (ACTG) studies, A5272 and A5280, with paired saliva samples and complete data sets were assessed.

Methods: Paired saliva samples were evaluated for bacterial microbiome using 16S rDNA PCR followed by Illumina sequencing. Diversity and differential abundance was compared between groups. A random forest classification scheme was used to determine the contribution of parameters in classifying participants' CD4+ T-cell count.

Results: Bacterial communities demonstrated considerable variability both within participants and between timepoints, although they became more similar after 24 weeks of ART. At baseline, both the number of taxa detected and the average alpha diversity were variable between participants, but did not differ significantly based on CD4+ cell count, viral load or other factors. After 24 weeks of ART samples obtained from participants with persistently low CD4+ T-cell counts had significantly higher bacterial richness and diversity. Several differentially abundant taxa, including Porphyromonas species associated with periodontal disease, were identified, which discriminated between baseline and posttreatment samples. Analysis demonstrated that although inflammatory markers are important in untreated disease, the salivary microbiome may play an important role in CD4+ T-cell count recovery after ART.

Conclusion: Shifts in the oral microbiome after ART initiation are complex, and may play an important role in immune function and inflammatory disease.
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http://dx.doi.org/10.1097/QAD.0000000000001811DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6198320PMC
June 2018

Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children.

Proc Natl Acad Sci U S A 2017 07 10;114(30):E6166-E6175. Epub 2017 Jul 10.

Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110;

Viruses have long been considered potential triggers of autoimmune diseases. Here we defined the intestinal virome from birth to the development of autoimmunity in children at risk for type 1 diabetes (T1D). A total of 220 virus-enriched preparations from serially collected fecal samples from 11 children (cases) who developed serum autoantibodies associated with T1D (of whom five developed clinical T1D) were compared with samples from controls. Intestinal viromes of case subjects were less diverse than those of controls. Among eukaryotic viruses, we identified significant enrichment of -related sequences in samples from controls in comparison with cases. Enterovirus, kobuvirus, parechovirus, parvovirus, and rotavirus sequences were frequently detected but were not associated with autoimmunity. For bacteriophages, we found higher Shannon diversity and richness in controls compared with cases and observed that changes in the intestinal virome over time differed between cases and controls. Using Random Forests analysis, we identified disease-associated viral bacteriophage contigs after subtraction of age-associated contigs. These disease-associated contigs were statistically linked to specific components of the bacterial microbiome. Thus, changes in the intestinal virome preceded autoimmunity in this cohort. Specific components of the virome were both directly and inversely associated with the development of human autoimmune disease.
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http://dx.doi.org/10.1073/pnas.1706359114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5544325PMC
July 2017

VirusSeeker, a computational pipeline for virus discovery and virome composition analysis.

Virology 2017 03 18;503:21-30. Epub 2017 Jan 18.

Departments of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA. Electronic address:

The advent of Next Generation Sequencing (NGS) has vastly increased our ability to discover novel viruses and to systematically define the spectrum of viruses present in a given specimen. Such studies have led to the discovery of novel viral pathogens as well as broader associations of the virome with diverse diseases including inflammatory bowel disease, severe acute malnutrition and HIV/AIDS. Critical to the success of these efforts are robust bioinformatic pipelines for rapid classification of microbial sequences. Existing computational tools are typically focused on either eukaryotic virus discovery or virome composition analysis but not both. Here we present VirusSeeker, a BLAST-based NGS data analysis pipeline designed for both purposes. VirusSeeker has been successfully applied in several previously published virome studies. Here we demonstrate the functionality of VirusSeeker in both novel virus discovery and virome composition analysis.
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http://dx.doi.org/10.1016/j.virol.2017.01.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5326578PMC
March 2017

Lactobacillus-Deficient Cervicovaginal Bacterial Communities Are Associated with Increased HIV Acquisition in Young South African Women.

Immunity 2017 01 10;46(1):29-37. Epub 2017 Jan 10.

Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital, Cambridge, MA 02139, USA; Harvard Medical School, Boston, MA 02115, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02115, USA. Electronic address:

Elevated inflammation in the female genital tract is associated with increased HIV risk. Cervicovaginal bacteria modulate genital inflammation; however, their role in HIV susceptibility has not been elucidated. In a prospective cohort of young, healthy South African women, we found that individuals with diverse genital bacterial communities dominated by anaerobes other than Gardnerella were at over 4-fold higher risk of acquiring HIV and had increased numbers of activated mucosal CD4 T cells compared to those with Lactobacillus crispatus-dominant communities. We identified specific bacterial taxa linked with reduced (L. crispatus) or elevated (Prevotella, Sneathia, and other anaerobes) inflammation and HIV infection and found that high-risk bacteria increased numbers of activated genital CD4 T cells in a murine model. Our results suggest that highly prevalent genital bacteria increase HIV risk by inducing mucosal HIV target cells. These findings might be leveraged to reduce HIV acquisition in women living in sub-Saharan Africa.
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http://dx.doi.org/10.1016/j.immuni.2016.12.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5270628PMC
January 2017

SIV Infection-Mediated Changes in Gastrointestinal Bacterial Microbiome and Virome Are Associated with Immunodeficiency and Prevented by Vaccination.

Cell Host Microbe 2016 Mar;19(3):323-35

Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA. Electronic address:

AIDS caused by simian immunodeficiency virus (SIV) infection is associated with gastrointestinal disease, systemic immune activation, and, in cross-sectional studies, changes in the enteric virome. Here we performed a longitudinal study of a vaccine cohort to define the natural history of changes in the fecal metagenome in SIV-infected monkeys. Matched rhesus macaques were either uninfected or intrarectally challenged with SIV, with a subset receiving the Ad26 vaccine, an adenovirus vector expressing the viral Env/Gag/Pol antigens. Progression of SIV infection to AIDS was associated with increased detection of potentially pathogenic viruses and bacterial enteropathogens. Specifically, adenoviruses were associated with an increased incidence of gastrointestinal disease and AIDS-related mortality. Viral and bacterial enteropathogens were largely absent from animals protected by the vaccine. These data suggest that the SIV-associated gastrointestinal disease is associated with the presence of both viral and bacterial enteropathogens and that protection against SIV infection by vaccination prevents enteropathogen emergence.
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http://dx.doi.org/10.1016/j.chom.2016.02.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4802495PMC
March 2016

Early life dynamics of the human gut virome and bacterial microbiome in infants.

Nat Med 2015 Oct 14;21(10):1228-34. Epub 2015 Sep 14.

Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA.

The early years of life are important for immune development and influence health in adulthood. Although it has been established that the gut bacterial microbiome is rapidly acquired after birth, less is known about the viral microbiome (or 'virome'), consisting of bacteriophages and eukaryotic RNA and DNA viruses, during the first years of life. Here, we characterized the gut virome and bacterial microbiome in a longitudinal cohort of healthy infant twins. The virome and bacterial microbiome were more similar between co-twins than between unrelated infants. From birth to 2 years of age, the eukaryotic virome and the bacterial microbiome expanded, but this was accompanied by a contraction of and shift in the bacteriophage virome composition. The bacteriophage-bacteria relationship begins from birth with a high predator-low prey dynamic, consistent with the Lotka-Volterra prey model. Thus, in contrast to the stable microbiome observed in adults, the infant microbiome is highly dynamic and associated with early life changes in the composition of bacteria, viruses and bacteriophages with age.
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http://dx.doi.org/10.1038/nm.3950DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4710368PMC
October 2015

Disease-specific alterations in the enteric virome in inflammatory bowel disease.

Cell 2015 Jan 22;160(3):447-60. Epub 2015 Jan 22.

Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA. Electronic address:

Decreases in the diversity of enteric bacterial populations are observed in patients with Crohn's disease (CD) and ulcerative colitis (UC). Less is known about the virome in these diseases. We show that the enteric virome is abnormal in CD and UC patients. In-depth analysis of preparations enriched for free virions in the intestine revealed that CD and UC were associated with a significant expansion of Caudovirales bacteriophages. The viromes of CD and UC patients were disease and cohort specific. Importantly, it did not appear that expansion and diversification of the enteric virome was secondary to changes in bacterial populations. These data support a model in which changes in the virome may contribute to intestinal inflammation and bacterial dysbiosis. We conclude that the virome is a candidate for contributing to, or being a biomarker for, human inflammatory bowel disease and speculate that the enteric virome may play a role in other diseases.
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http://dx.doi.org/10.1016/j.cell.2015.01.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4312520PMC
January 2015

Pathogenic simian immunodeficiency virus infection is associated with expansion of the enteric virome.

Cell 2012 Oct;151(2):253-66

Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA.

Pathogenic simian immunodeficiency virus (SIV) infection is associated with enteropathy, which likely contributes to AIDS progression. To identify candidate etiologies for AIDS enteropathy, we used next-generation sequencing to define the enteric virome during SIV infection in nonhuman primates. Pathogenic, but not nonpathogenic, SIV infection was associated with significant expansion of the enteric virome. We identified at least 32 previously undescribed enteric viruses during pathogenic SIV infection and confirmed their presence by using viral culture and PCR testing. We detected unsuspected mucosal adenovirus infection associated with enteritis as well as parvovirus viremia in animals with advanced AIDS, indicating the pathogenic potential of SIV-associated expansion of the enteric virome. No association between pathogenic SIV infection and the family-level taxonomy of enteric bacteria was detected. Thus, enteric viral infections may contribute to AIDS enteropathy and disease progression. These findings underline the importance of metagenomic analysis of the virome for understanding AIDS pathogenesis.
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http://dx.doi.org/10.1016/j.cell.2012.09.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3490196PMC
October 2012

Specific mutation of a gammaherpesvirus-expressed antigen in response to CD8 T cell selection in vivo.

J Virol 2012 Mar 14;86(5):2887-93. Epub 2011 Dec 14.

Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.

Herpesviruses are thought to be highly genetically stable, and their use as vaccine vectors has been proposed. However, studies of the human gammaherpesvirus, Epstein-Barr virus, have found viral isolates containing mutations in HLA class I-restricted epitopes. Using murine gammaherpesvirus 68 expressing ovalbumin (OVA), we examined the stability of a gammaherpesvirus antigenic locus under strong CD8 T cell selection in vivo. OVA-specific CD8 T cells selected viral isolates containing mutations in the OVA locus but minimal alterations in other genomic regions. Thus, a CD8 T cell response to a gammaherpesvirus-expressed antigen that is not essential for replication or pathogenesis can result in selective mutation of that antigen in vivo. This finding may have relevance for the use of herpesvirus vectors for chronic antigen expression in vivo.
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http://dx.doi.org/10.1128/JVI.06101-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3302239PMC
March 2012

Gammaherpesvirus gene expression and DNA synthesis are facilitated by viral protein kinase and histone variant H2AX.

Virology 2011 Nov 22;420(2):73-81. Epub 2011 Sep 22.

Department of Microbiology and Molecular Genetics, Cancer Center, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226, USA.

Gammaherpesvirus protein kinases are an attractive therapeutic target as they support lytic replication and latency. Via an unknown mechanism these kinases enhance expression of select viral genes and DNA synthesis. Importantly, the kinase phenotypes have not been examined in primary cell types. Mouse gammaherpesvirus-68 (MHV68) protein kinase orf36 activates the DNA damage response (DDR) and facilitates lytic replication in primary macrophages. Significantly, H2AX, a DDR component and putative orf36 substrate, enhances MHV68 replication. Here we report that orf36 facilitated expression of RTA, an immediate early MHV68 gene, and DNA synthesis during de novo infection of primary macrophages. H2AX expression supported efficient RTA transcription and phosphorylated H2AX associated with RTA promoter. Furthermore, viral DNA synthesis was attenuated in H2AX-deficient macrophages, suggesting that the DDR system was exploited throughout the replication cycle. The interactions between a cancer-associated gammaherpesvirus and host tumor suppressor system have important implications for the pathogenesis of gammaherpesvirus infection.
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http://dx.doi.org/10.1016/j.virol.2011.08.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204369PMC
November 2011

The genome of Yoka poxvirus.

J Virol 2011 Oct 3;85(19):10230-8. Epub 2011 Aug 3.

Department of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.

Yoka poxvirus was isolated almost four decades ago from a mosquito pool in the Central African Republic. Its classification as a poxvirus is based solely upon the morphology of virions visualized by electron microscopy. Here we describe sequencing of the Yoka poxvirus genome using a combination of Roche/454 and Illumina next-generation sequencing technologies. A single consensus contig of ∼175 kb in length that encodes 186 predicted genes was generated. Multiple methods were used to show that Yoka poxvirus is most closely related to viruses in the Orthopoxvirus genus, but it is clearly distinct from previously described poxviruses. Collectively, the phylogenetic and genomic sequence analyses suggest that Yoka poxvirus is the prototype member of a new genus in the family Poxviridae.
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http://dx.doi.org/10.1128/JVI.00637-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3196448PMC
October 2011

Identification and sequencing of a novel rodent gammaherpesvirus that establishes acute and latent infection in laboratory mice.

J Virol 2011 Mar 5;85(6):2642-56. Epub 2011 Jan 5.

Department of Pathology and Immunology, Washington University School of Medicine, 660 S. Euclid Ave., Box 8118, St. Louis, MO 63110, USA.

Gammaherpesviruses encode numerous immunomodulatory molecules that contribute to their ability to evade the host immune response and establish persistent, lifelong infections. As the human gammaherpesviruses are strictly species specific, small animal models of gammaherpesvirus infection, such as murine gammaherpesvirus 68 (γHV68) infection, are important for studying the roles of gammaherpesvirus immune evasion genes in in vivo infection and pathogenesis. We report here the genome sequence and characterization of a novel rodent gammaherpesvirus, designated rodent herpesvirus Peru (RHVP), that shares conserved genes and genome organization with γHV68 and the primate gammaherpesviruses but is phylogenetically distinct from γHV68. RHVP establishes acute and latent infection in laboratory mice. Additionally, RHVP contains multiple open reading frames (ORFs) not present in γHV68 that have sequence similarity to primate gammaherpesvirus immunomodulatory genes or cellular genes. These include ORFs with similarity to major histocompatibility complex class I (MHC-I), C-type lectins, and the mouse mammary tumor virus and herpesvirus saimiri superantigens. As these ORFs may function as immunomodulatory or virulence factors, RHVP presents new opportunities for the study of mechanisms of immune evasion by gammaherpesviruses.
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http://dx.doi.org/10.1128/JVI.01661-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3067950PMC
March 2011

Detection of novel sequences related to african Swine Fever virus in human serum and sewage.

J Virol 2009 Dec 7;83(24):13019-25. Epub 2009 Oct 7.

Department of Pathology & Immunology, Washington University School of Medicine, 660 S. Euclid Ave., Box 8118, St. Louis, MO 63110, USA.

The family Asfarviridae contains only a single virus species, African swine fever virus (ASFV). ASFV is a viral agent with significant economic impact due to its devastating effects on populations of domesticated pigs during outbreaks but has not been reported to infect humans. We report here the discovery of novel viral sequences in human serum and sewage which are clearly related to the asfarvirus family but highly divergent from ASFV. Detection of these sequences suggests that greater genetic diversity may exist among asfarviruses than previously thought and raises the possibility that human infection by asfarviruses may occur.
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http://dx.doi.org/10.1128/JVI.00638-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2786824PMC
December 2009