Publications by authors named "Joseph L DeRisi"

206 Publications

POECIVIRUS IS PRESENT IN INDIVIDUALS WITH BEAK DEFORMITIES IN SEVEN SPECIES OF NORTH AMERICAN BIRDS.

J Wildl Dis 2021 Apr;57(2):273-281

Department of Biochemistry and Biophysics, University of California, 1700 4th Street, QB3 Room 404, San Francisco, California 94158, USA.

Avian keratin disorder (AKD), a disease of unknown etiology characterized by debilitating beak overgrowth, has increasingly affected wild bird populations since the 1990s. A novel picornavirus, poecivirus, is closely correlated with disease status in Black-capped Chickadees (Poecile atricapillus) in Alaska, US. However, our knowledge of the relationship between poecivirus and beak deformities in other species and other geographic areas remains limited. The growing geographic scope and number of species affected by AKD-like beak deformities require a better understanding of the causative agent to evaluate the population-level impacts of this epizootic. Here, we tested eight individuals from six avian species with AKD-consistent deformities for the presence of poecivirus: Mew Gull (Larus canus), Hairy Woodpecker (Picoides villosus), Black-billed Magpie (Pica hudsonia), American Crow (Corvus brachyrhynchos), Red-breasted Nuthatch (Sitta canadensis), and Blackpoll Warbler (Setophaga striata). The birds were sampled in Alaska and Maine (1999-2016). We used targeted PCR followed by Sanger sequencing to test for the presence of poecivirus in each specimen and to obtain viral genome sequence from virus-positive host individuals. We detected poecivirus in all individuals tested, but not in negative controls (water and tissue samples). Furthermore, we used unbiased metagenomic sequencing to test for the presence of other pathogens in six of these specimens (Hairy Woodpecker, two American Crows, two Red-breasted Nuthatches, Blackpoll Warbler). This analysis yielded additional viral sequences from several specimens, including the complete coding region of poecivirus from one Red-breasted Nuthatch, which we confirmed via targeted PCR followed by Sanger sequencing. This study demonstrates that poecivirus is present in individuals with AKD-consistent deformities from six avian species other than Black-capped Chickadee. While further investigation will be required to explore whether there exists a causal link between this virus and AKD, this study demonstrates that poecivirus is not geographically restricted to Alaska, but rather occurs elsewhere in North America.
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http://dx.doi.org/10.7589/JWD-D-20-00017DOI Listing
April 2021

Impaired antibacterial immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19.

medRxiv 2021 Mar 26. Epub 2021 Mar 26.

Secondary bacterial infections, including ventilator-associated pneumonia (VAP), lead to worse clinical outcomes and increased mortality following viral respiratory infections. Critically ill patients with coronavirus disease 2019 (COVID-19) face an elevated risk of VAP, although susceptibility varies widely. Because mechanisms underlying VAP predisposition remained unknown, we assessed lower respiratory tract host immune responses and microbiome dynamics in 36 patients, including 28 COVID-19 patients, 15 of whom developed VAP, and eight critically ill controls. We employed a combination of tracheal aspirate bulk and single cell RNA sequencing (scRNA-seq). Two days before VAP onset, a lower respiratory transcriptional signature of bacterial infection was observed, characterized by increased expression of neutrophil degranulation, toll-like receptor and cytokine signaling pathways. When assessed at an earlier time point following endotracheal intubation, more than two weeks prior to VAP onset, we observed a striking early impairment in antibacterial innate and adaptive immune signaling that markedly differed from COVID-19 patients who did not develop VAP. scRNA-seq further demonstrated suppressed immune signaling across monocytes/macrophages, neutrophils and T cells. While viral load did not differ at an early post-intubation timepoint, impaired SARS-CoV-2 clearance and persistent interferon signaling characterized the patients who later developed VAP. Longitudinal metatranscriptomic analysis revealed disruption of lung microbiome community composition in patients who developed VAP, providing a connection between dysregulated immune signaling and outgrowth of opportunistic pathogens. Together, these findings demonstrate that COVID-19 patients who develop VAP have impaired antibacterial immune defense weeks before secondary infection onset.

One Sentence Summary: COVID-19 patients with secondary bacterial pneumonia have impaired immune signaling and lung microbiome changes weeks before onset.
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http://dx.doi.org/10.1101/2021.03.23.21253487DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8010763PMC
March 2021

Genome-Wide Ribosome Profiling of the Plasmodium falciparum Intraerythrocytic Developmental Cycle.

Methods Mol Biol 2021 ;2252:57-87

Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.

Monitoring whole-genome translation and mRNA ribosome occupancy in vivo using ribosome profiling has proven to be a powerful tool for discovery of gene expression regulation, mechanisms of translation, and new open reading frames, in a wide range of different cell types in different organisms. Here we describe its application to the malaria parasite, Plasmodium falciparum. We present methods for intact polysome purification from parasite cultures, polysome digestion, monosome purification, ribosome footprint nucleic acid extraction, and Illumina library preparation.
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http://dx.doi.org/10.1007/978-1-0716-1150-0_3DOI Listing
January 2021

Persistence of ambigrammatic narnaviruses requires translation of the reverse open reading frame.

J Virol 2021 Mar 24. Epub 2021 Mar 24.

Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA

Narnaviruses are RNA viruses detected in diverse fungi, plants, protists, arthropods and nematodes. Though initially described as simple single-gene non-segmented viruses encoding RNA-dependent RNA polymerase (RdRp), a subset of narnaviruses referred to as "ambigrammatic" harbor a unique genomic configuration consisting of overlapping open reading frames (ORFs) encoded on opposite strands. Phylogenetic analysis supports selection to maintain this unusual genome organization, but functional investigations are lacking. Here, we establish the mosquito-infecting Culex narnavirus 1 (CxNV1) as a model to investigate the functional role of overlapping ORFs in narnavirus replication. In CxNV1, a reverse ORF without homology to known proteins covers nearly the entire 3.2 kb segment encoding the RdRp. Additionally, two opposing and nearly completely overlapping novel ORFs are found on the second putative CxNV1 segment, the 0.8 kb "Robin" RNA. We developed a system to launch CxNV1 in a naïve mosquito cell line, then showed that functional RdRp is required for persistence of both segments, and an intact reverse ORF is required on the RdRp segment for persistence. Mass spectrometry of persistently CxNV1-infected cells provided evidence for translation of this reverse ORF. Finally, ribosome profiling yielded a striking pattern of footprints for all four CxNV1 RNA strands that was distinct from actively-translating ribosomes on host mRNA or co-infecting RNA viruses. Taken together, these data raise the possibility that the process of translation itself is important for persistence of ambigrammatic narnaviruses, potentially by protecting viral RNA with ribosomes, thus suggesting a heretofore undescribed viral tactic for replication and transmission.Fundamental to our understanding of RNA viruses is a description of which strand(s) of RNA are transmitted as the viral genome, relative to which encode the viral proteins. Ambigrammatic narnaviruses break the mold. These viruses, found broadly in fungi, plants, and insects, have the unique feature of two overlapping genes encoded on opposite strands, comprising nearly the full length of the viral genome. Such extensive overlap is not seen in other RNA viruses, and comes at the cost of reduced evolutionary flexibility in the sequence. The present study is motivated by investigating the benefits which balance that cost. We show for the first time a functional requirement for the ambigrammatic genome configuration in Culex narnavirus 1, which suggests a model for how translation of both strands might benefit this virus. Our work highlights a new blueprint for viral persistence, distinct from strategies defined by canonical definitions of the coding strand.
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http://dx.doi.org/10.1128/JVI.00109-21DOI Listing
March 2021

Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19.

bioRxiv 2021 Mar 10. Epub 2021 Mar 10.

Type I interferon (IFN-I) neutralizing autoantibodies have been found in some critical COVID-19 patients; however, their prevalence and longitudinal dynamics across the disease severity scale, and functional effects on circulating leukocytes remain unknown. Here, in 284 COVID-19 patients, we found IFN-I autoantibodies in 19% of critical, 6% of severe and none of the moderate cases. Longitudinal profiling of over 600,000 peripheral blood mononuclear cells using multiplexed single-cell epitope and transcriptome sequencing from 54 COVID-19 patients, 15 non-COVID-19 patients and 11 non-hospitalized healthy controls, revealed a lack of IFN-I stimulated gene (ISG-I) response in myeloid cells from critical cases, including those producing anti-IFN-I autoantibodies. Moreover, surface protein analysis showed an inverse correlation of the inhibitory receptor LAIR-1 with ISG-I expression response early in the disease course. This aberrant ISG-I response in critical patients with and without IFN-I autoantibodies, supports a unifying model for disease pathogenesis involving ISG-I suppression via convergent mechanisms.
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http://dx.doi.org/10.1101/2021.03.09.434529DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7987018PMC
March 2021

Cerebrospinal fluid pterins, pterin-dependent neurotransmitters, and mortality in pediatric cerebral malaria.

J Infect Dis 2021 Feb 22. Epub 2021 Feb 22.

Department of Medicine, University of Utah School of Medicine and VA Medical Center, Salt Lake City, UT, United States.

Background: Cerebral malaria (CM) pathogenesis remains incompletely understood. Having shown low systemic levels of tetrahydrobiopterin (BH4), an enzymatic cofactor for neurotransmitter synthesis, we hypothesized that BH4 and BH4-dependent neurotransmitters would likewise be low in cerebrospinal fluid (CSF) in CM.

Methods: We prospectively enrolled Tanzanian children with CM and children with non-malaria central nervous system conditions (NMC). We measured CSF levels of BH4, neopterin, and BH4-dependent neurotransmitter metabolites, 3-O-methyldopa, homovanillic acid, and 5-hydroxyindoleacetate, and derived age-adjusted z-scores using published reference ranges.

Results: CSF BH4 was elevated in CM (n=49) compared to NMC (n=51) [z-score 0.75 vs. -0.08 (p<0.001)]. Neopterin was increased in CM [z-score 4.05 vs. 0.09 (p<0.001)], and a cut-off at the upper limit of normal (60 nmol/L) was 100% sensitive for CM. Neurotransmitter metabolite levels were overall preserved. A higher CSF BH4:BH2 ratio was associated with increased odds of survival (OR 2.94 [1.03-8.33]; p=0.043).

Conclusion: Despite low systemic BH4, CSF BH4 was elevated and associated with increased odds of survival in CM. Coma in malaria is not explained by deficiency of BH4-dependent neurotransmitters. Elevated CSF neopterin was 100% sensitive for CM diagnosis, and warrants further assessment of its clinical utility for ruling out CM in malaria-endemic areas.
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http://dx.doi.org/10.1093/infdis/jiab086DOI Listing
February 2021

The COVID-19 epidemic in Madagascar: clinical description and laboratory results of the first wave, march-september 2020.

Influenza Other Respir Viruses 2021 Feb 15. Epub 2021 Feb 15.

Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar.

Background: Following the first detection of SARS-CoV-2 in passengers arriving from Europe on 19 March 2020, Madagascar took several mitigation measures to limit the spread of the virus in the country.

Methods: Nasopharyngeal and/or oropharyngeal swabs were collected from travellers to Madagascar, suspected SARS-CoV-2 cases and contact of confirmed cases. Swabs were tested at the national reference laboratory using real-time RT-PCR. Data collected from patients were entered in an electronic database for subsequent statistical analysis. All distribution of laboratory-confirmed cases were mapped, and six genomes of viruses were fully sequenced.

Results: Overall, 26,415 individuals were tested for SARS-CoV-2 between 18 March and 18 September 2020, of whom 21.0% (5,553/26,145) returned positive. Among laboratory-confirmed SARS-CoV-2-positive patients, the median age was 39 years (IQR: 28-52), and 56.6% (3,311/5,553) were asymptomatic at the time of sampling. The probability of testing positive increased with age with the highest adjusted odds ratio of 2.2 [95% CI: 1.9-2.5] for individuals aged 49 years and more. Viral strains sequenced belong to clades 19A, 20A and 20B indicative of several independent introduction of viruses.

Conclusions: Our study describes the first wave of the COVID-19 in Madagascar. Despite early strategies in place Madagascar could not avoid the introduction and spread of the virus. More studies are needed to estimate the true burden of disease and make public health recommendations for a better preparation to another wave.
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http://dx.doi.org/10.1111/irv.12845DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8013501PMC
February 2021

Nasopharyngeal SARS-CoV-2 viral loads in young children do not differ significantly from those in older children and adults.

Sci Rep 2021 02 4;11(1):3044. Epub 2021 Feb 4.

Chan-Zuckerberg Biohub, San Francisco, CA, USA.

The role of children in the spread of the SARS-CoV-2 coronavirus has become a matter of urgent debate as societies in the US and abroad consider how to safely reopen schools. Small studies have suggested higher viral loads in young children. Here we present a multicenter investigation on over five thousand SARS-CoV-2 cases confirmed by real-time reverse transcription (RT) PCR assay. Notably, we found no discernable difference in amount of viral nucleic acid among young children and adults.
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http://dx.doi.org/10.1038/s41598-021-81934-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7862672PMC
February 2021

The pulmonary metatranscriptome prior to pediatric HCT identifies post-HCT lung injury.

Blood 2021 Mar;137(12):1679-1689

Department of Biochemistry and Biophysics, School of Medicine.

Lung injury after pediatric allogeneic hematopoietic cell transplantation (HCT) is a common and disastrous complication that threatens long-term survival. To develop strategies to prevent lung injury, novel tools are needed to comprehensively assess lung health in HCT candidates. Therefore, this study analyzed biospecimens from 181 pediatric HCT candidates who underwent routine pre-HCT bronchoalveolar lavage (BAL) at the University Medical Center Utrecht between 2005 and 2016. BAL fluid underwent metatranscriptomic sequencing of microbial and human RNA, and unsupervised clustering and generalized linear models were used to associate microbiome gene expression data with the development of post-HCT lung injury. Microbe-gene correlations were validated using a geographically distinct cohort of 18 pediatric HCT candidates. The cumulative incidence of post-HCT lung injury varied significantly according to 4 pre-HCT pulmonary metatranscriptome clusters, with the highest incidence observed in children with pre-HCT viral enrichment and innate immune activation, as well as in children with profound microbial depletion and concomitant natural killer/T-cell activation (P < .001). In contrast, children with pre-HCT pulmonary metatranscriptomes containing diverse oropharyngeal taxa and lacking inflammation rarely developed post-HCT lung injury. In addition, activation of epithelial-epidermal differentiation, mucus production, and cellular adhesion were associated with fatal post-HCT lung injury. In a separate validation cohort, associations among pulmonary respiratory viral load, oropharyngeal taxa, and pulmonary gene expression were recapitulated; the association with post-HCT lung injury needs to be validated in an independent cohort. This analysis suggests that assessment of the pre-HCT BAL fluid may identify high-risk pediatric HCT candidates who may benefit from pathobiology-targeted interventions.
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http://dx.doi.org/10.1182/blood.2020009246DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7995292PMC
March 2021

Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy.

Cell 2021 01 4;184(2):323-333.e9. Epub 2020 Dec 4.

J. David Gladstone Institutes, San Francisco, CA 94158, USA; Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA. Electronic address:

The December 2019 outbreak of a novel respiratory virus, SARS-CoV-2, has become an ongoing global pandemic due in part to the challenge of identifying symptomatic, asymptomatic, and pre-symptomatic carriers of the virus. CRISPR diagnostics can augment gold-standard PCR-based testing if they can be made rapid, portable, and accurate. Here, we report the development of an amplification-free CRISPR-Cas13a assay for direct detection of SARS-CoV-2 from nasal swab RNA that can be read with a mobile phone microscope. The assay achieved ∼100 copies/μL sensitivity in under 30 min of measurement time and accurately detected pre-extracted RNA from a set of positive clinical samples in under 5 min. We combined crRNAs targeting SARS-CoV-2 RNA to improve sensitivity and specificity and directly quantified viral load using enzyme kinetics. Integrated with a reader device based on a mobile phone, this assay has the potential to enable rapid, low-cost, point-of-care screening for SARS-CoV-2.
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http://dx.doi.org/10.1016/j.cell.2020.12.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7834310PMC
January 2021

Upper airway gene expression reveals suppressed immune responses to SARS-CoV-2 compared with other respiratory viruses.

Nat Commun 2020 11 17;11(1):5854. Epub 2020 Nov 17.

Division of Infectious Diseases, University of California, San Francisco, CA, USA.

SARS-CoV-2 infection is characterized by peak viral load in the upper airway prior to or at the time of symptom onset, an unusual feature that has enabled widespread transmission of the virus and precipitated a global pandemic. How SARS-CoV-2 is able to achieve high titer in the absence of symptoms remains unclear. Here, we examine the upper airway host transcriptional response in patients with COVID-19 (n = 93), other viral (n = 41) or non-viral (n = 100) acute respiratory illnesses (ARIs). Compared with other viral ARIs, COVID-19 is characterized by a pronounced interferon response but attenuated activation of other innate immune pathways, including toll-like receptor, interleukin and chemokine signaling. The IL-1 and NLRP3 inflammasome pathways are markedly less responsive to SARS-CoV-2, commensurate with a signature of diminished neutrophil and macrophage recruitment. This pattern resembles previously described distinctions between symptomatic and asymptomatic viral infections and may partly explain the propensity for pre-symptomatic transmission in COVID-19. We further use machine learning to build 27-, 10- and 3-gene classifiers that differentiate COVID-19 from other ARIs with AUROCs of 0.981, 0.954 and 0.885, respectively. Classifier performance is stable across a wide range of viral load, suggesting utility in mitigating false positive or false negative results of direct SARS-CoV-2 tests.
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http://dx.doi.org/10.1038/s41467-020-19587-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7673985PMC
November 2020

Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids.

Nat Med 2021 01 9;27(1):115-124. Epub 2020 Nov 9.

Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.

We developed a metagenomic next-generation sequencing (mNGS) test using cell-free DNA from body fluids to identify pathogens. The performance of mNGS testing of 182 body fluids from 160 patients with acute illness was evaluated using two sequencing platforms in comparison to microbiological testing using culture, 16S bacterial PCR and/or 28S-internal transcribed ribosomal gene spacer (28S-ITS) fungal PCR. Test sensitivity and specificity of detection were 79 and 91% for bacteria and 91 and 89% for fungi, respectively, by Illumina sequencing; and 75 and 81% for bacteria and 91 and 100% for fungi, respectively, by nanopore sequencing. In a case series of 12 patients with culture/PCR-negative body fluids but for whom an infectious diagnosis was ultimately established, seven (58%) were mNGS positive. Real-time computational analysis enabled pathogen identification by nanopore sequencing in a median 50-min sequencing and 6-h sample-to-answer time. Rapid mNGS testing is a promising tool for diagnosis of unknown infections from body fluids.
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http://dx.doi.org/10.1038/s41591-020-1105-zDOI Listing
January 2021

Rapid deployment of SARS-CoV-2 testing: The CLIAHUB.

Authors:
Emily D Crawford Irene Acosta Vida Ahyong Erika C Anderson Shaun Arevalo Daniel Asarnow Shannon Axelrod Patrick Ayscue Camillia S Azimi Caleigh M Azumaya Stefanie Bachl Iris Bachmutsky Aparna Bhaduri Jeremy Bancroft Brown Joshua Batson Astrid Behnert Ryan M Boileau Saumya R Bollam Alain R Bonny David Booth Michael Jerico B Borja David Brown Bryan Buie Cassandra E Burnett Lauren E Byrnes Katelyn A Cabral Joana P Cabrera Saharai Caldera Gabriela Canales Gloria R Castañeda Agnes Protacio Chan Christopher R Chang Arthur Charles-Orszag Carly Cheung Unseng Chio Eric D Chow Y Rose Citron Allison Cohen Lillian B Cohn Charles Chiu Mitchel A Cole Daniel N Conrad Angela Constantino Andrew Cote Tre'Jon Crayton-Hall Spyros Darmanis Angela M Detweiler Rebekah L Dial Shen Dong Elias M Duarte David Dynerman Rebecca Egger Alison Fanton Stacey M Frumm Becky Xu Hua Fu Valentina E Garcia Julie Garcia Christina Gladkova Miriam Goldman Rafael Gomez-Sjoberg M Grace Gordon James C R Grove Shweta Gupta Alexis Haddjeri-Hopkins Pierce Hadley John Haliburton Samantha L Hao George Hartoularos Nadia Herrera Melissa Hilberg Kit Ying E Ho Nicholas Hoppe Shayan Hosseinzadeh Conor J Howard Jeffrey A Hussmann Elizabeth Hwang Danielle Ingebrigtsen Julia R Jackson Ziad M Jowhar Danielle Kain James Y S Kim Amy Kistler Oriana Kreutzfeld Jessie Kulsuptrakul Andrew F Kung Charles Langelier Matthew T Laurie Lena Lee Kun Leng Kristoffer E Leon Manuel D Leonetti Sophia R Levan Sam Li Aileen W Li Jamin Liu Heidi S Lubin Amy Lyden Jennifer Mann Sabrina Mann Gorica Margulis Diana M Marquez Bryan P Marsh Calla Martyn Elizabeth E McCarthy Aaron McGeever Alexander F Merriman Lauren K Meyer Steve Miller Megan K Moore Cody T Mowery Tanzila Mukhtar Lusajo L Mwakibete Noelle Narez Norma F Neff Lindsay A Osso Diter Oviedo Suping Peng Maira Phelps Kiet Phong Peter Picard Lindsey M Pieper Neha Pincha Angela Oliveira Pisco Angela Pogson Sergei Pourmal Robert R Puccinelli Andreas S Puschnik Elze Rackaityte Preethi Raghavan Madhura Raghavan James Reese Joseph M Replogle Hanna Retallack Helen Reyes Donald Rose Marci F Rosenberg Estella Sanchez-Guerrero Sydney M Sattler Laura Savy Stephanie K See Kristin K Sellers Paula Hayakawa Serpa Maureen Sheehy Jonathan Sheu Sukrit Silas Jessica A Streithorst Jack Strickland Doug Stryke Sara Sunshine Peter Suslow Renaldo Sutanto Serena Tamura Michelle Tan Jiongyi Tan Alice Tang Cristina M Tato Jack C Taylor Iliana Tenvooren Erin M Thompson Edward C Thornborrow Eric Tse Tony Tung Marc L Turner Victoria S Turner Rigney E Turnham Mary J Turocy Trisha V Vaidyanathan Ilia D Vainchtein Manu Vanaerschot Sara E Vazquez Anica M Wandler Anne Wapniarski James T Webber Zara Y Weinberg Alexandra Westbrook Allison W Wong Emily Wong Gajus Worthington Fang Xie Albert Xu Terrina Yamamoto Ying Yang Fauna Yarza Yefim Zaltsman Tina Zheng Joseph L DeRisi

PLoS Pathog 2020 10 28;16(10):e1008966. Epub 2020 Oct 28.

Chan Zuckerberg Biohub, San Francisco, California, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1008966DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7592773PMC
October 2020

IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring.

Gigascience 2020 10;9(10)

Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA.

Background: Metagenomic next-generation sequencing (mNGS) has enabled the rapid, unbiased detection and identification of microbes without pathogen-specific reagents, culturing, or a priori knowledge of the microbial landscape. mNGS data analysis requires a series of computationally intensive processing steps to accurately determine the microbial composition of a sample. Existing mNGS data analysis tools typically require bioinformatics expertise and access to local server-class hardware resources. For many research laboratories, this presents an obstacle, especially in resource-limited environments.

Findings: We present IDseq, an open source cloud-based metagenomics pipeline and service for global pathogen detection and monitoring (https://idseq.net). The IDseq Portal accepts raw mNGS data, performs host and quality filtration steps, then executes an assembly-based alignment pipeline, which results in the assignment of reads and contigs to taxonomic categories. The taxonomic relative abundances are reported and visualized in an easy-to-use web application to facilitate data interpretation and hypothesis generation. Furthermore, IDseq supports environmental background model generation and automatic internal spike-in control recognition, providing statistics that are critical for data interpretation. IDseq was designed with the specific intent of detecting novel pathogens. Here, we benchmark novel virus detection capability using both synthetically evolved viral sequences and real-world samples, including IDseq analysis of a nasopharyngeal swab sample acquired and processed locally in Cambodia from a tourist from Wuhan, China, infected with the recently emergent SARS-CoV-2.

Conclusion: The IDseq Portal reduces the barrier to entry for mNGS data analysis and enables bench scientists, clinicians, and bioinformaticians to gain insight from mNGS datasets for both known and novel pathogens.
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http://dx.doi.org/10.1093/gigascience/giaa111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7566497PMC
October 2020

Temporal airway microbiome changes related to ventilator-associated pneumonia in children.

Eur Respir J 2021 Mar 18;57(3). Epub 2021 Mar 18.

Biostatistics and Informatics, University of Colorado, Colorado School of Public Health, Aurora, CO, USA.

We sought to determine whether temporal changes in the lower airway microbiome are associated with ventilator-associated pneumonia (VAP) in children.Using a multicentre prospective study of children aged 31 days to 18 years requiring mechanical ventilation support for >72 h, daily tracheal aspirates were collected and analysed by sequencing of the 16S rRNA gene. VAP was assessed using 2008 Centers for Disease Control and Prevention paediatric criteria. The association between microbial factors and VAP was evaluated using joint longitudinal time-to-event modelling, matched case-control comparisons and unsupervised clustering.Out of 366 eligible subjects, 66 (15%) developed VAP at a median of 5 (interquartile range 3-5) days post intubation. At intubation, there was no difference in total bacterial load (TBL), but Shannon diversity and the relative abundance of , Lactobacillales and were lower for VAP subjects non-VAP subjects. However, higher TBL on each sequential day was associated with a lower hazard (hazard ratio 0.39, 95% CI 0.23-0.64) for developing VAP, but sequential values of diversity were not associated with VAP. Similar findings were observed from the matched analysis and unsupervised clustering. The most common dominant VAP pathogens included species (19%), (14%) and / (10%). and were also identified as dominant organisms in several subjects.In mechanically ventilated children, changes over time in microbial factors were marginally associated with VAP risk, although these changes were not suitable for predicting VAP in individual patients. These findings suggest that focusing exclusively on pathogen burden may not adequately inform VAP diagnosis.
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http://dx.doi.org/10.1183/13993003.01829-2020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7979474PMC
March 2021

ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens.

Cell Rep Med 2020 Oct 24;1(7):100123. Epub 2020 Sep 24.

Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.

Comprehensive understanding of the serological response to SARS-CoV-2 infection is important for both pathophysiologic insight and diagnostic development. Here, we generate a pan-human coronavirus programmable phage display assay to perform proteome-wide profiling of coronavirus antigens enriched by 98 COVID-19 patient sera. Next, we use ReScan, a method to efficiently sequester phage expressing the most immunogenic peptides and print them onto paper-based microarrays using acoustic liquid handling, which isolates and identifies nine candidate antigens, eight of which are derived from the two proteins used for SARS-CoV-2 serologic assays: spike and nucleocapsid proteins. After deployment in a high-throughput assay amenable to clinical lab settings, these antigens show improved specificity over a whole protein panel. This proof-of-concept study demonstrates that ReScan will have broad applicability for other emerging infectious diseases or autoimmune diseases that lack a valid biomarker, enabling a seamless pipeline from antigen discovery to diagnostic using one recombinant protein source.
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http://dx.doi.org/10.1016/j.xcrm.2020.100123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7513813PMC
October 2020

Deep profiling of protease substrate specificity enabled by dual random and scanned human proteome substrate phage libraries.

Proc Natl Acad Sci U S A 2020 10 24;117(41):25464-25475. Epub 2020 Sep 24.

Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158;

Proteolysis is a major posttranslational regulator of biology inside and outside of cells. Broad identification of optimal cleavage sites and natural substrates of proteases is critical for drug discovery and to understand protease biology. Here, we present a method that employs two genetically encoded substrate phage display libraries coupled with next generation sequencing (SPD-NGS) that allows up to 10,000-fold deeper sequence coverage of the typical six- to eight-residue protease cleavage sites compared to state-of-the-art synthetic peptide libraries or proteomics. We applied SPD-NGS to two classes of proteases, the intracellular caspases, and the ectodomains of the sheddases, ADAMs 10 and 17. The first library (Lib 10AA) allowed us to identify 10 to 10 unique cleavage sites over a 1,000-fold dynamic range of NGS counts and produced consensus and optimal cleavage motifs based position-specific scoring matrices. A second SPD-NGS library (Lib hP), which displayed virtually the entire human proteome tiled in contiguous 49 amino acid sequences with 25 amino acid overlaps, enabled us to identify candidate human proteome sequences. We identified up to 10 natural linear cut sites, depending on the protease, and captured most of the examples previously identified by proteomics and predicted 10- to 100-fold more. Structural bioinformatics was used to facilitate the identification of candidate natural protein substrates. SPD-NGS is rapid, reproducible, simple to perform and analyze, inexpensive, and renewable, with unprecedented depth of coverage for substrate sequences, and is an important tool for protease biologists interested in protease specificity for specific assays and inhibitors and to facilitate identification of natural protein substrates.
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http://dx.doi.org/10.1073/pnas.2009279117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7568340PMC
October 2020

High-resolution epitope mapping of anti-Hu and anti-Yo autoimmunity by programmable phage display.

Brain Commun 2020 3;2(2):fcaa059. Epub 2020 Aug 3.

Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.

Paraneoplastic neurological disorders are immune-mediated diseases understood to manifest as part of a misdirected anti-tumor immune response. Paraneoplastic neurological disorder-associated autoantibodies can assist with diagnosis and enhance our understanding of tumor-associated immune processes. We designed a comprehensive library of 49-amino-acid overlapping peptides spanning the entire human proteome, including all splicing isoforms and computationally predicted coding regions. Using this library, we optimized a phage immunoprecipitation and sequencing protocol with multiple rounds of enrichment to create high-resolution epitope profiles in serum and cerebrospinal fluid (CSF) samples from patients suffering from two common paraneoplastic neurological disorders, the anti-Yo ( = 36 patients) and anti-Hu ( = 44 patients) syndromes. All (100%) anti-Yo patient samples yielded enrichment of peptides from the canonical anti-Yo (CDR2 and CDR2L) antigens, while 38% of anti-Hu patients enriched peptides deriving from the nELAVL (neuronal embryonic lethal abnormal vision like) family of proteins, the anti-Hu autoantigenic target. Among the anti-Hu patient samples that were positive for nELAVL, we noted a restricted region of immunoreactivity. To achieve single amino acid resolution, we designed a novel deep mutational scanning phage library encoding all possible single-point mutants targeting the reactive nELAVL region. This analysis revealed a distinct preference for the degenerate motif, RLDxLL, shared by ELAVL2, 3 and 4. Lastly, phage immunoprecipitation sequencing identified several known autoantigens in these same patient samples, including peptides deriving from the cancer-associated antigens ZIC and SOX families of transcription factors. Overall, this optimized phage immunoprecipitation sequencing library and protocol yielded the high-resolution epitope mapping of the autoantigens targeted in anti-Yo and anti-Hu encephalitis patients to date. The results presented here further demonstrate the utility and high-resolution capability of phage immunoprecipitation sequencing for both basic science and clinical applications and for better understanding the antigenic targets and triggers of paraneoplastic neurological disorders.
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http://dx.doi.org/10.1093/braincomms/fcaa059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7425417PMC
August 2020

Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: A retrospective cohort study of patients with and without COVID-19.

EClinicalMedicine 2020 Oct 26;27:100518. Epub 2020 Aug 26.

Division of Infectious Diseases, University of California, San Francisco, CA, USA.

Background: Most data on the clinical presentation, diagnostics, and outcomes of patients with COVID-19 have been presented as case series without comparison to patients with other acute respiratory illnesses.

Methods: We examined emergency department patients between February 3 and March 31, 2020 with an acute respiratory illness who were tested for SARS-CoV-2. We determined COVID-19 status by PCR and metagenomic next generation sequencing (mNGS). We compared clinical presentation, diagnostics, treatment, and outcomes.

Findings: Among 316 patients, 33 tested positive for SARS-CoV-2; 31 without COVID-19 tested positive for another respiratory virus. Among patients with additional viral testing (27/33), no SARS-CoV-2 co-infections were identified. Compared to those who tested negative, patients with COVID-19 reported longer symptoms duration (median 7d vs. 3d,  < 0.001). Patients with COVID-19 were more often hospitalized (79% vs. 56%,  = 0.014). When hospitalized, patients with COVID-19 had longer hospitalizations (median 10.7d vs. 4.7d,  < 0.001) and more often developed ARDS (23% vs. 3%,  < 0.001). Most comorbidities, medications, symptoms, vital signs, laboratories, treatments, and outcomes did not differ by COVID-19 status.

Interpretation: While we found differences in clinical features of COVID-19 compared to other acute respiratory illnesses, there was significant overlap in presentation and comorbidities. Patients with COVID-19 were more likely to be admitted to the hospital, have longer hospitalizations and develop ARDS, and were unlikely to have co-existent viral infections.

Funding: National Center for Advancing Translational Sciences, National Heart Lung Blood Institute, National Institute of Allergy and Infectious Diseases, Chan Zuckerberg Biohub, Chan Zuckerberg Initiative.
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http://dx.doi.org/10.1016/j.eclinm.2020.100518DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7447618PMC
October 2020

A pathogenic and clonally expanded B cell transcriptome in active multiple sclerosis.

Proc Natl Acad Sci U S A 2020 09 28;117(37):22932-22943. Epub 2020 Aug 28.

Weill Institute for Neurosciences, University of California, San Francisco, CA 94158;

Central nervous system B cells have several potential roles in multiple sclerosis (MS): secretors of proinflammatory cytokines and chemokines, presenters of autoantigens to T cells, producers of pathogenic antibodies, and reservoirs for viruses that trigger demyelination. To interrogate these roles, single-cell RNA sequencing (scRNA-Seq) was performed on paired cerebrospinal fluid (CSF) and blood from subjects with relapsing-remitting MS (RRMS; = 12), other neurologic diseases (ONDs; = 1), and healthy controls (HCs; = 3). Single-cell immunoglobulin sequencing (scIg-Seq) was performed on a subset of these subjects and additional RRMS ( = 4), clinically isolated syndrome ( = 2), and OND ( = 2) subjects. Further, paired CSF and blood B cell subsets (RRMS; = 7) were isolated using fluorescence activated cell sorting for bulk RNA sequencing (RNA-Seq). Independent analyses across technologies demonstrated that nuclear factor kappa B (NF-κB) and cholesterol biosynthesis pathways were activated, and specific cytokine and chemokine receptors were up-regulated in CSF memory B cells. Further, SMAD/TGF-β1 signaling was down-regulated in CSF plasmablasts/plasma cells. Clonally expanded, somatically hypermutated IgM+ and IgG1+ CSF B cells were associated with inflammation, blood-brain barrier breakdown, and intrathecal Ig synthesis. While we identified memory B cells and plasmablast/plasma cells with highly similar Ig heavy-chain sequences across MS subjects, similarities were also identified with ONDs and HCs. No viral transcripts, including from Epstein-Barr virus, were detected. Our findings support the hypothesis that in MS, CSF B cells are driven to an inflammatory and clonally expanded memory and plasmablast/plasma cell phenotype.
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http://dx.doi.org/10.1073/pnas.2008523117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7502747PMC
September 2020

Erratum.

Authors:
Joseph L DeRisi

Pediatr Dent 2020 07;42(4):248

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July 2020

Expanded Clinical Phenotype, Oncological Associations, and Immunopathologic Insights of Paraneoplastic Kelch-like Protein-11 Encephalitis.

JAMA Neurol 2020 Aug 3. Epub 2020 Aug 3.

Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.

Importance: Recognizing the presenting and immunopathological features of Kelch-like protein-11 immunoglobulin G seropositive (KLHL11 IgG+) patients may aid in early diagnosis and management.

Objective: To describe expanding neurologic phenotype, cancer associations, outcomes, and immunopathologic features of KLHL11 encephalitis.

Design, Setting, And Participants: This retrospective tertiary care center study, conducted from October 15, 1998, to November 1, 2019, prospectively identified 31 KLHL11 IgG+ cases in the neuroimmunology laboratory. Eight were identified by retrospective testing of patients with rhomboencephalitis (confirmed by tissue-based-immunofluorescence and transfected-cell-based assays).

Main Outcomes And Measures: Outcome variables included modified Rankin score and gait aid use.

Results: All 39 KLHL11 IgG+ patients were men (median age, 46 years; range, 28-73 years). Initial clinical presentations were ataxia (n = 32; 82%), diplopia (n = 22; 56%), vertigo (n = 21; 54%), hearing loss (n = 15; 39%), tinnitus (n = 14; 36%), dysarthria (n = 11; 28%), and seizures (n = 9; 23%). Atypical neurologic presentations included neuropsychiatric dysfunction, myeloneuropathy, and cervical amyotrophy. Hearing loss or tinnitus preceded other neurologic deficits by 1 to 8 months in 10 patients (26%). Among patients screened for malignancy (n = 36), testicular germ-cell tumors (n = 23; 64%) or testicular microlithiasis and fibrosis concerning for regressed germ cell tumor (n = 7; 19%) were found in 83% of the patients (n = 30). In 2 patients, lymph node biopsy diagnosed metastatic lung adenocarcinoma in one and chronic lymphocytic leukemia in the other. Initial brain magnetic resonance imaging revealed T2 hyperintensities in the temporal lobe (n = 12), cerebellum (n = 9), brainstem (n = 3), or diencephalon (n = 3). Among KLHL11 IgG+ patients who underwent HLA class I and class II genotyping (n = 10), most were found to have HLA-DQB1*02:01 (n = 7; 70%) and HLA-DRB1*03:01 (n = 6; 60%) associations. A biopsied gadolinium-enhancing temporal lobe lesion demonstrated T cell-predominant inflammation and nonnecrotizing granulomas. Cerebellar biopsy (patient with chronic ataxia) and 2 autopsied brains demonstrated Purkinje neuronal loss and Bergmann gliosis, supporting early active inflammation and later extensive neuronal loss. Compared with nonautoimmune control peripheral blood mononuclear cells, cluster of differentiation (CD) 8+ and CD4+ T cells were significantly activated when patient peripheral blood mononuclear cells were cultured with KLHL11 protein. Most patients (58%) benefitted from immunotherapy and/or cancer treatment (neurological disability stabilized [n = 10] or improved [n = 9]). Kaplan-Meier curve demonstrated significantly higher probability of wheelchair dependence among patients without detectable testicular cancer. Long-term outcomes in KLHL11-IgG+ patients were similar to Ma2 encephalitis.

Conclusions And Relevance: Kelch-like protein-11 IgG is a biomarker of testicular germ-cell tumor and paraneoplastic neurologic syndrome, often refractory to treatment. Described expanded neurologic phenotype and paraclinical findings may aid in its early diagnosis and treatment.
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http://dx.doi.org/10.1001/jamaneurol.2020.2231DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7653501PMC
August 2020

Genomic Profiling of Evolving Daptomycin Resistance in a Patient with Recurrent Staphylococcus argenteus Sepsis.

Antimicrob Agents Chemother 2020 09 21;64(10). Epub 2020 Sep 21.

Chan Zuckerberg Biohub, San Francisco, California, USA

is a novel staphylococcal species associated with invasive disease. We report the first case of daptomycin/vancomycin-resistant , initially speciated as , that developed from repeated treatment with daptomycin for a complex vascular graft infection. Whole-genome sequencing of longitudinally collected isolates identified acquisition of MprF S337L, a mutation predicted to increase surface charge and repel cationic molecules.
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http://dx.doi.org/10.1128/AAC.00961-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7508626PMC
September 2020

Complete Genome Sequence of a Novel Coronavirus (SARS-CoV-2) Isolate from Bangladesh.

Microbiol Resour Announc 2020 Jun 11;9(24). Epub 2020 Jun 11.

Child Health Research Foundation, Dhaka, Bangladesh.

The complete genome sequence of a novel coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) isolate obtained from a nasopharyngeal swab from a patient with COVID-19 in Bangladesh is reported.
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http://dx.doi.org/10.1128/MRA.00568-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7291105PMC
June 2020

Enhanced Tooth Structure Via Silver Microwires Following Treatment with 38 Percent Silver Diamine Fluoride.

Pediatr Dent 2020 May;42(3):226-231

Dr. DeRisi is a professor, in the Department of Biochemistry and Biophysics, University of California San Francisco and co-president of the Chan-Zuckerberg BioHub, San Francisco, Calif., USA.

American Academy of Pediatric Dentistry guidelines recommend treatment of primary teeth with 38 percent silver diamine fluoride (SDF) as a noninvasive option to arrest active dental caries lesions. A significant outcome of SDF treatment are lesions that clinically harden and become more resistant to further decay. Many practicing dentists believe that this increased hardening is due to the reaction of silver and fluoride with carious dentin. The purpose of this study was to focus on the structural and chemical effects of silver diamine fluoride treatment on the native tooth. In SDF-treated cavitated dentin lesions in teeth subsequently extracted for orthodontic reasons, the authors observed continuous, filamentous silver densities formed in situ from 50 to 2,100 μm in length and 0.25 to 7.0 μm in diameter using high-resolution synchrotron X-ray microcomputer tomography and field emission scanning electron microscopy. These "microwires" fill voids in the lesion caused by disease and permeate through surrounding dentinal tubules. Spectroscopy confirmed that the chemical composition of the observed microwires is predominantly silver. These observations suggest mechanistic explanations for the structural reinforcement of carious dentin in addition to remineralization. It is hypothesized that silver diamine fluoride may achieve its antimicrobial functions by biochemical interactions and through its inherent ability to integrate into the native tooth structure.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7295027PMC
May 2020

Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: a comparison of patients with and without COVID-19.

medRxiv 2020 May 6. Epub 2020 May 6.

Background: Emerging data on the clinical presentation, diagnostics, and outcomes of patients with COVID-19 have largely been presented as case series. Few studies have compared these clinical features and outcomes of COVID-19 to other acute respiratory illnesses.

Methods: We examined all patients presenting to an emergency department in San Francisco, California between February 3 and March 31, 2020 with an acute respiratory illness who were tested for SARS-CoV-2. We determined COVID-19 status by PCR and metagenomic next generation sequencing (mNGS). We compared demographics, comorbidities, symptoms, vital signs, and laboratory results including viral diagnostics using PCR and mNGS. Among those hospitalized, we determined differences in treatment (antibiotics, antivirals, respiratory support) and outcomes (ICU admission, ICU interventions, acute respiratory distress syndrome, cardiac injury).

Findings: In a cohort of 316 patients, 33 (10%) tested positive for SARS-CoV-2; 31 patients, all without COVID-19, tested positive for another respiratory virus (16%). Among patients with additional viral testing, no co-infections with SARS-CoV-2 were identified by PCR or mNGS. Patients with COVID-19 reported longer symptoms duration (median 7 vs. 3 days), and were more likely to report fever (82% vs. 44%), fatigue (85% vs. 50%), and myalgias (61% vs 27%); p<0.001 for all comparisons. Lymphopenia (55% vs 34%, p=0.018) and bilateral opacities on initial chest radiograph (55% vs. 24%, p=0.001) were more common in patients with COVID-19. Patients with COVID-19 were more often hospitalized (79% vs. 56%, p=0.014). Of 186 hospitalized patients, patients with COVID-19 had longer hospitalizations (median 10.7d vs. 4.7d, p<0.001) and were more likely to develop ARDS (23% vs. 3%, p<0.001). Most comorbidities, home medications, signs and symptoms, vital signs, laboratory results, treatment, and outcomes did not differ by COVID-19 status.

Interpretation: While we found differences in clinical features of COVID-19 compared to other acute respiratory illnesses, there was significant overlap in presentation and comorbidities. Patients with COVID-19 were more likely to be admitted to the hospital, have longer hospitalizations and develop ARDS, and were unlikely to have co-existent viral infections. These findings enhance understanding of the clinical characteristics of COVID-19 in comparison to other acute respiratory illnesses.  .
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http://dx.doi.org/10.1101/2020.05.02.20082461DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7273256PMC
May 2020

Upper airway gene expression differentiates COVID-19 from other acute respiratory illnesses and reveals suppression of innate immune responses by SARS-CoV-2.

medRxiv 2020 May 19. Epub 2020 May 19.

Division of Infectious Diseases, University of California, San Francisco, CA, USA.

We studied the host transcriptional response to SARS-CoV-2 by performing metagenomic sequencing of upper airway samples in 238 patients with COVID-19, other viral or non-viral acute respiratory illnesses (ARIs). Compared to other viral ARIs, COVID-19 was characterized by a diminished innate immune response, with reduced expression of genes involved in toll-like receptor and interleukin signaling, chemokine binding, neutrophil degranulation and interactions with lymphoid cells. Patients with COVID-19 also exhibited significantly reduced proportions of neutrophils and macrophages, and increased proportions of goblet, dendritic and B-cells, compared to other viral ARIs. Using machine learning, we built 26-, 10- and 3-gene classifiers that differentiated COVID-19 from other acute respiratory illnesses with AUCs of 0.980, 0.950 and 0.871, respectively. Classifier performance was stable at low viral loads, suggesting utility in settings where direct detection of viral nucleic acid may be unsuccessful. Taken together, our results illuminate unique aspects of the host transcriptional response to SARS-CoV-2 in comparison to other respiratory viruses and demonstrate the feasibility of COVID-19 diagnostics based on patient gene expression.
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http://dx.doi.org/10.1101/2020.05.18.20105171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7273244PMC
May 2020

Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia.

bioRxiv 2020 Mar 5. Epub 2020 Mar 5.

Virology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia.

Rapid production and publication of pathogen genome sequences during emerging disease outbreaks provide crucial public health information. In resource-limited settings, especially near an outbreak epicenter, conventional deep sequencing or bioinformatics are often challenging. Here we successfully used metagenomic next generation sequencing on an iSeq100 Illumina platform paired with an open-source bioinformatics pipeline to quickly characterize Cambodia's first case of COVID-2019.
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http://dx.doi.org/10.1101/2020.03.02.968818DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217139PMC
March 2020

Identification of novel, clinically correlated autoantigens in the monogenic autoimmune syndrome APS1 by proteome-wide PhIP-Seq.

Elife 2020 05 15;9. Epub 2020 May 15.

Diabetes Center, University of California, San Francisco, San Francisco, United States.

The identification of autoantigens remains a critical challenge for understanding and treating autoimmune diseases. Autoimmune polyendocrine syndrome type 1 (APS1), a rare monogenic form of autoimmunity, presents as widespread autoimmunity with T and B cell responses to multiple organs. Importantly, autoantibody discovery in APS1 can illuminate fundamental disease pathogenesis, and many of the antigens found in APS1 extend to more common autoimmune diseases. Here, we performed proteome-wide programmable phage-display (PhIP-Seq) on sera from a cohort of people with APS1 and discovered multiple common antibody targets. These novel APS1 autoantigens exhibit tissue-restricted expression, including expression in enteroendocrine cells, pineal gland, and dental enamel. Using detailed clinical phenotyping, we find novel associations between autoantibodies and organ-restricted autoimmunity, including a link between anti-KHDC3L autoantibodies and premature ovarian insufficiency, and between anti-RFX6 autoantibodies and diarrheal-type intestinal dysfunction. Our study highlights the utility of PhIP-Seq for extensively interrogating antigenic repertoires in human autoimmunity and the importance of antigen discovery for improved understanding of disease mechanisms.
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http://dx.doi.org/10.7554/eLife.55053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7228772PMC
May 2020