1
|
Servellita V, Sotomayor Gonzalez A, Lamson DM, Foresythe A, Huh HJ, Bazinet AL, Bergman NH, Bull RL, Garcia KY, Goodrich JS, Lovett SP, Parker K, Radune D, Hatada A, Pan CY, Rizzo K, Bertumen JB, Morales C, Oluniyi PE, Nguyen J, Tan J, Stryke D, Jaber R, Leslie MT, Lyons Z, Hedman HD, Parashar U, Sullivan M, Wroblewski K, Oberste MS, Tate JE, Baker JM, Sugerman D, Potts C, Lu X, Chhabra P, Ingram LA, Shiau H, Britt W, Gutierrez Sanchez LH, Ciric C, Rostad CA, Vinjé J, Kirking HL, Wadford DA, Raborn RT, St George K, Chiu CY. Adeno-associated virus type 2 in US children with acute severe hepatitis. Nature 2023; 617:574-580. [PMID: 36996871 PMCID: PMC10170441 DOI: 10.1038/s41586-023-05949-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 03/10/2023] [Indexed: 04/01/2023]
Abstract
As of August 2022, clusters of acute severe hepatitis of unknown aetiology in children have been reported from 35 countries, including the USA1,2. Previous studies have found human adenoviruses (HAdVs) in the blood from patients in Europe and the USA3-7, although it is unclear whether this virus is causative. Here we used PCR testing, viral enrichment-based sequencing and agnostic metagenomic sequencing to analyse samples from 16 HAdV-positive cases from 1 October 2021 to 22 May 2022, in parallel with 113 controls. In blood from 14 cases, adeno-associated virus type 2 (AAV2) sequences were detected in 93% (13 of 14), compared to 4 (3.5%) of 113 controls (P < 0.001) and to 0 of 30 patients with hepatitis of defined aetiology (P < 0.001). In controls, HAdV type 41 was detected in blood from 9 (39.1%) of the 23 patients with acute gastroenteritis (without hepatitis), including 8 of 9 patients with positive stool HAdV testing, but co-infection with AAV2 was observed in only 3 (13.0%) of these 23 patients versus 93% of cases (P < 0.001). Co-infections by Epstein-Barr virus, human herpesvirus 6 and/or enterovirus A71 were also detected in 12 (85.7%) of 14 cases, with higher herpesvirus detection in cases versus controls (P < 0.001). Our findings suggest that the severity of the disease is related to co-infections involving AAV2 and one or more helper viruses.
Collapse
Affiliation(s)
- Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | - Daryl M Lamson
- Wadsworth Center, New York State Department of Health, David Axelrod Institute, Albany, NY, USA
| | - Abiodun Foresythe
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Hee Jae Huh
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Adam L Bazinet
- National Biodefense Analysis and Countermeasures Center (NBACC), Frederick, MD, USA
| | - Nicholas H Bergman
- National Biodefense Analysis and Countermeasures Center (NBACC), Frederick, MD, USA
| | - Robert L Bull
- Federal Bureau of Investigation Laboratory Division/Scientific Response and Analysis Unit, Quantico, VA, USA
| | - Karla Y Garcia
- National Biodefense Analysis and Countermeasures Center (NBACC), Frederick, MD, USA
| | - Jennifer S Goodrich
- National Biodefense Analysis and Countermeasures Center (NBACC), Frederick, MD, USA
| | - Sean P Lovett
- National Biodefense Analysis and Countermeasures Center (NBACC), Frederick, MD, USA
| | - Kisha Parker
- National Biodefense Analysis and Countermeasures Center (NBACC), Frederick, MD, USA
| | - Diana Radune
- National Biodefense Analysis and Countermeasures Center (NBACC), Frederick, MD, USA
| | - April Hatada
- California Department of Public Health, Richmond, CA, USA
| | - Chao-Yang Pan
- California Department of Public Health, Richmond, CA, USA
| | - Kyle Rizzo
- California Department of Public Health, Richmond, CA, USA
| | - J Bradford Bertumen
- California Department of Public Health, Richmond, CA, USA
- Centers for Disease Control and Prevention, Atlanta, CA, USA
| | | | - Paul E Oluniyi
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jenny Nguyen
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jessica Tan
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Doug Stryke
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Rayah Jaber
- Florida Department of Health, Tallahassee, FL, USA
| | | | - Zin Lyons
- North Carolina Department of Health and Human Services, Raleigh, NC, USA
| | - Hayden D Hedman
- Centers for Disease Control and Prevention, Atlanta, CA, USA
- South Dakota Department of Health, Pierre, SD, USA
| | - Umesh Parashar
- Centers for Disease Control and Prevention, Atlanta, CA, USA
| | - Maureen Sullivan
- Association for Public Health Laboratories, Silver Spring, MD, USA
| | - Kelly Wroblewski
- Association for Public Health Laboratories, Silver Spring, MD, USA
| | | | | | - Julia M Baker
- Centers for Disease Control and Prevention, Atlanta, CA, USA
| | - David Sugerman
- Centers for Disease Control and Prevention, Atlanta, CA, USA
| | - Caelin Potts
- Centers for Disease Control and Prevention, Atlanta, CA, USA
| | - Xiaoyan Lu
- Centers for Disease Control and Prevention, Atlanta, CA, USA
| | - Preeti Chhabra
- Centers for Disease Control and Prevention, Atlanta, CA, USA
| | | | - Henry Shiau
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - William Britt
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Caroline Ciric
- Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Christina A Rostad
- Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Jan Vinjé
- Centers for Disease Control and Prevention, Atlanta, CA, USA
| | | | | | - R Taylor Raborn
- National Biodefense Analysis and Countermeasures Center (NBACC), Frederick, MD, USA
| | - Kirsten St George
- Wadsworth Center, New York State Department of Health, David Axelrod Institute, Albany, NY, USA
- Department of Biomedical Science, University at Albany, SUNY, Albany, NY, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
| |
Collapse
|
2
|
Ye Z, Zhao C, Raborn RT, Lin M, Wei W, Hao Y, Lynch M. Genetic Diversity, Heteroplasmy, and Recombination in Mitochondrial Genomes of Daphnia pulex, Daphnia pulicaria, and Daphnia obtusa. Mol Biol Evol 2022; 39:6553573. [PMID: 35325186 PMCID: PMC9004417 DOI: 10.1093/molbev/msac059] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genetic variants of mitochondrial DNA at the individual (heteroplasmy) and population (polymorphism) levels provide insight into their roles in multiple cellular and evolutionary processes. However, owing to the paucity of genome-wide data at the within-individual and population levels, the broad patterns of these two forms of variation remain poorly understood. Here, we analyze 1,804 complete mitochondrial genome sequences from Daphnia pulex, Daphnia pulicaria, and Daphnia obtusa. Extensive heteroplasmy is observed in D. obtusa, where the high level of intraclonal divergence must have resulted from a biparental-inheritance event, and recombination in the mitochondrial genome is apparent, although perhaps not widespread. Global samples of D. pulex reveal remarkably low mitochondrial effective population sizes, <3% of those for the nuclear genome. In addition, levels of population diversity in mitochondrial and nuclear genomes are uncorrelated across populations, suggesting an idiosyncratic evolutionary history of mitochondria in D. pulex. These population-genetic features appear to be a consequence of background selection associated with highly deleterious mutations arising in the strongly linked mitochondrial genome, which is consistent with polymorphism and divergence data suggesting a predominance of strong purifying selection. Nonetheless, the fixation of mildly deleterious mutations in the mitochondrial genome also appears to be driving positive selection on genes encoded in the nuclear genome whose products are deployed in the mitochondrion.
Collapse
Affiliation(s)
- Zhiqiang Ye
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ, 85287
| | - Chaoxian Zhao
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ, 85287
| | - R Taylor Raborn
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ, 85287
| | - Man Lin
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ, 85287
| | - Wen Wei
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ, 85287
| | - Yue Hao
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ, 85287
| | - Michael Lynch
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ, 85287
| |
Collapse
|
3
|
Luo D, Huguet-Tapia JC, Raborn RT, White FF, Brendel VP, Yang B. The Xa7 resistance gene guards the rice susceptibility gene SWEET14 against exploitation by the bacterial blight pathogen. Plant Commun 2021; 2:100164. [PMID: 34027391 PMCID: PMC8132128 DOI: 10.1016/j.xplc.2021.100164] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 05/03/2023]
Abstract
Many plant disease resistance (R) genes function specifically in reaction to the presence of cognate effectors from a pathogen. Xanthomonas oryzae pathovar oryzae (Xoo) uses transcription activator-like effectors (TALes) to target specific rice genes for expression, thereby promoting host susceptibility to bacterial blight. Here, we report the molecular characterization of Xa7, the cognate R gene to the TALes AvrXa7 and PthXo3, which target the rice major susceptibility gene SWEET14. Xa7 was mapped to a unique 74-kb region. Gene expression analysis of the region revealed a candidate gene that contained a putative AvrXa7 effector binding element (EBE) in its promoter and encoded a 113-amino-acid peptide of unknown function. Genome editing at the Xa7 locus rendered the plants susceptible to avrXa7-carrying Xoo strains. Both AvrXa7 and PthXo3 activated a GUS reporter gene fused with the EBE-containing Xa7 promoter in Nicotiana benthamiana. The EBE of Xa7 is a close mimic of the EBE of SWEET14 for TALe-induced disease susceptibility. Ectopic expression of Xa7 triggers cell death in N. benthamiana. Xa7 is prevalent in indica rice accessions from 3000 rice genomes. Xa7 appears to be an adaptation that protects against pathogen exploitation of SWEET14 and disease susceptibility.
Collapse
Affiliation(s)
- Dangping Luo
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Jose C. Huguet-Tapia
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - R. Taylor Raborn
- Department of Biology, Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
- Current address: Biodesign Institute Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
| | - Frank F. White
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Volker P. Brendel
- Department of Biology, Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Corresponding author
| |
Collapse
|
5
|
Raborn RT, Spitze K, Brendel VP, Lynch M. Promoter Architecture and Sex-Specific Gene Expression in Daphnia pulex. Genetics 2016; 204:593-612. [PMID: 27585846 PMCID: PMC5068849 DOI: 10.1534/genetics.116.193334] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 07/29/2016] [Indexed: 11/18/2022] Open
Abstract
Large-scale transcription start site (TSS) profiling produces a high-resolution, quantitative picture of transcription initiation and core promoter locations within a genome. However, application of TSS profiling to date has largely been restricted to a small set of prominent model systems. We sought to characterize the cis-regulatory landscape of the water flea Daphnia pulex, an emerging model arthropod that reproduces both asexually (via parthenogenesis) and sexually (via meiosis). We performed Cap Analysis of Gene Expression (CAGE) with RNA isolated from D. pulex within three developmental states: sexual females, asexual females, and males. Identified TSSs were utilized to generate a "Daphnia Promoter Atlas," i.e., a catalog of active promoters across the surveyed states. Analysis of the distribution of promoters revealed evidence for widespread alternative promoter usage in D. pulex, in addition to a prominent fraction of compactly-arranged promoters in divergent orientations. We carried out de novo motif discovery using CAGE-defined TSSs and identified eight candidate core promoter motifs; this collection includes canonical promoter elements (e.g., TATA and Initiator) in addition to others lacking obvious orthologs. A comparison of promoter activities found evidence for considerable state-specific differential gene expression between states. Our work represents the first global definition of transcription initiation and promoter architecture in crustaceans. The Daphnia Promoter Atlas presented here provides a valuable resource for comparative study of cis-regulatory regions in metazoans, as well as for investigations into the circuitries that underpin meiosis and parthenogenesis.
Collapse
Affiliation(s)
- R Taylor Raborn
- Department of Biology, Indiana University, Bloomington, Indiana 47405 School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405
| | - Ken Spitze
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Volker P Brendel
- Department of Biology, Indiana University, Bloomington, Indiana 47405 School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| |
Collapse
|