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Martinů J, Tarabai H, Štefka J, Hypša V. Highly Resolved Genomes of Two Closely Related Lineages of the Rodent Louse Polyplax serrata with Different Host Specificities. Genome Biol Evol 2024; 16:evae045. [PMID: 38478715 PMCID: PMC10972687 DOI: 10.1093/gbe/evae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2024] [Indexed: 04/01/2024] Open
Abstract
Sucking lice of the parvorder Anoplura are permanent ectoparasites with specific lifestyle and highly derived features. Currently, genomic data are only available for a single species, the human louse Pediculus humanus. Here, we present genomes of two distinct lineages, with different host spectra, of a rodent louse Polyplax serrata. Genomes of these ecologically different lineages are closely similar in gene content and display a conserved order of genes, with the exception of a single translocation. Compared with P. humanus, the P. serrata genomes are noticeably larger (139 vs. 111 Mbp) and encode a higher number of genes. Similar to P. humanus, they are reduced in sensory-related categories such as vision and olfaction. Utilizing genome-wide data, we perform phylogenetic reconstruction and evolutionary dating of the P. serrata lineages. Obtained estimates reveal their relatively deep divergence (∼6.5 Mya), comparable with the split between the human and chimpanzee lice P. humanus and Pediculus schaeffi. This supports the view that the P. serrata lineages are likely to represent two cryptic species with different host spectra. Historical demographies show glaciation-related population size (Ne) reduction, but recent restoration of Ne was seen only in the less host-specific lineage. Together with the louse genomes, we analyze genomes of their bacterial symbiont Legionella polyplacis and evaluate their potential complementarity in synthesis of amino acids and B vitamins. We show that both systems, Polyplax/Legionella and Pediculus/Riesia, display almost identical patterns, with symbionts involved in synthesis of B vitamins but not amino acids.
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Affiliation(s)
- Jana Martinů
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Hassan Tarabai
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Central European Institute of Technology (CEITEC), University of Veterinary Sciences, Brno, Czech Republic
| | - Jan Štefka
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Parasitology, Biology Centre, The Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Václav Hypša
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Parasitology, Biology Centre, The Czech Academy of Sciences, České Budějovice, Czech Republic
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Herzog KS, Hackett JL, Hime PM, Klicka LB, Jensen K. First Insights into Population Structure and Genetic Diversity Versus Host Specificity in Trypanorhynch Tapeworms Using Multiplexed Shotgun Genotyping. Genome Biol Evol 2023; 15:evad190. [PMID: 37906040 PMCID: PMC10616631 DOI: 10.1093/gbe/evad190] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Accepted: 10/13/2023] [Indexed: 11/02/2023] Open
Abstract
Theory predicts relaxed host specificity and high host vagility should contribute to reduced genetic structure in parasites while strict host specificity and low host vagility should increase genetic structure. Though these predictions are intuitive, they have never been explicitly tested in a population genomic framework. Trypanorhynch tapeworms, which parasitize sharks and rays (elasmobranchs) as definitive hosts, are the only order of elasmobranch tapeworms that exhibit considerable variability in their definitive host specificity. This allows for unique combinations of host use and geographic range, making trypanorhynchs ideal candidates for studying how these traits influence population-level structure and genetic diversity. Multiplexed shotgun genotyping (MSG) data sets were generated to characterize component population structure and infrapopulation diversity for a representative of each trypanorhynch suborder: the ray-hosted Rhinoptericola megacantha (Trypanobatoida) and the shark-hosted Callitetrarhynchus gracilis (Trypanoselachoida). Adults of R. megacantha are more host-specific and less broadly distributed than adults of C. gracilis, allowing correlation between these factors and genetic structure. Replicate tapeworm specimens were sequenced from the same host individual, from multiple conspecific hosts within and across geographic regions, and from multiple definitive host species. For R. megacantha, population structure coincided with geography rather than host species. For C. gracilis, limited population structure was found, suggesting a potential link between degree of host specificity and structure. Conspecific trypanorhynchs from the same host individual were found to be as, or more, genetically divergent from one another as from conspecifics from different host individuals. For both species, high levels of homozygosity and positive FIS values were documented.
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Affiliation(s)
- Kaylee S Herzog
- Department of Epidemiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, USA
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | | | - Paul M Hime
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, USA
| | - Lukas B Klicka
- School of Arts and Sciences, Peru State College, Nebraska, USA
| | - Kirsten Jensen
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, USA
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
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Meile L, Garrido-Arandia M, Bernasconi Z, Peter J, Schneller A, Bernasconi A, Alassimone J, McDonald BA, Sánchez-Vallet A. Natural variation in Avr3D1 from Zymoseptoria sp. contributes to quantitative gene-for-gene resistance and to host specificity. New Phytol 2023; 238:1562-1577. [PMID: 36529883 DOI: 10.1111/nph.18690] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 07/29/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Successful host colonization by plant pathogens requires the circumvention of host defense responses, frequently through sequence modifications in secreted pathogen proteins known as avirulence factors (Avrs). Although Avr sequences are often polymorphic, the contribution of these polymorphisms to virulence diversity in natural pathogen populations remains largely unexplored. We used molecular genetic tools to determine how natural sequence polymorphisms of the avirulence factor Avr3D1 in the wheat pathogen Zymoseptoria tritici contributed to adaptive changes in virulence. We showed that there is a continuous distribution in the magnitude of resistance triggered by different Avr3D1 isoforms and demonstrated that natural variation in an Avr gene can lead to a quantitative resistance phenotype. We further showed that homologues of Avr3D1 in two nonpathogenic sister species of Z. tritici are recognized by some wheat cultivars, suggesting that Avr-R gene-for-gene interactions can contribute to nonhost resistance. We suggest that the mechanisms underlying host range, qualitative resistance, and quantitative resistance are not exclusive.
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Affiliation(s)
- Lukas Meile
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223, Pozuelo de Alarcón, Madrid, Spain
| | - María Garrido-Arandia
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040, Madrid, Spain
| | - Zoe Bernasconi
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Jules Peter
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Alissa Schneller
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Alessio Bernasconi
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Julien Alassimone
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Andrea Sánchez-Vallet
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223, Pozuelo de Alarcón, Madrid, Spain
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Chiba Y, Sasaki M, Masuda S, Shibata A, Shirasu K, Kawaharada Y. A Novel Rhizobium sp. Chiba-1 Strain Exhibits a Host Range for Nodule Symbiosis in Lotus Species. Microbes Environ 2023; 38:ME23056. [PMID: 38044128 PMCID: PMC10728632 DOI: 10.1264/jsme2.me23056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/16/2023] [Indexed: 12/05/2023] Open
Abstract
Rhizobia are soil bacteria that induce the formation of nodules in the roots of leguminous plants for mutualistic establishment. Although the symbiotic mechanism between Lotus japonicus and its major symbiotic rhizobia, Mesorhizobium loti, has been extensively characterized, our understanding of symbiotic mechanisms, such as host specificity and host ranges, remains limited. In the present study, we isolated a novel Rhizobium strain capable of forming nodules on L. burttii from agricultural soil at Iwate prefecture in Japan. We conducted genomic and host range ana-lyses of various Lotus species. The results obtained revealed that the novel isolated Rhizobium sp. Chiba-1 was closely related to R. leguminosarum and had a wide host range that induced nodule development, including L. burttii and several L. japonicus wild-type accessions. However, L. japonicus Gifu exhibited an incompatible nodule phenotype. We also identified the formation of an epidermal infection threads that was dependent on the Lotus species and independent of nodule organ development. In conclusion, this newly isolated Rhizobium strain displays a distinct nodulation phenotype from Lotus species, and the results obtained herein provide novel insights into the functional mechanisms underlying host specificity and host ranges.
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Affiliation(s)
- Yuhei Chiba
- United Graduate School of Agricultural Sciences, Iwate University, 3–18–8, Ueda, Morioka, Iwate 020–8550, Japan
| | - Mao Sasaki
- Graduate School of Arts and Sciences, Iwate University, 3–18–8 Ueda, Morioka, Iwate 020–8550, Japan
| | - Sachiko Masuda
- RIKEN Center for Sustainable Resource Science, Yokohama, 230–0045, Japan
| | - Arisa Shibata
- RIKEN Center for Sustainable Resource Science, Yokohama, 230–0045, Japan
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama, 230–0045, Japan
| | - Yasuyuki Kawaharada
- United Graduate School of Agricultural Sciences, Iwate University, 3–18–8, Ueda, Morioka, Iwate 020–8550, Japan
- Graduate School of Arts and Sciences, Iwate University, 3–18–8 Ueda, Morioka, Iwate 020–8550, Japan
- Department of Plant BioSciences, Faculty of Agriculture, Iwate University, 3–18–8, Ueda, Morioka, 020–8550, Iwate, Japan
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Howell AA, Versoza CJ, Cerna G, Johnston T, Kakde S, Karuku K, Kowal M, Monahan J, Murray J, Nguyen T, Sanchez Carreon A, Streiff A, Su B, Youkhana F, Munig S, Patel Z, So M, Sy M, Weiss S, Pfeifer SP. Phylogenomic analyses and host range prediction of cluster P mycobacteriophages. G3 (Bethesda) 2022; 12:jkac244. [PMID: 36094333 PMCID: PMC9635641 DOI: 10.1093/g3journal/jkac244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
Bacteriophages, infecting bacterial hosts in every environment on our planet, are a driver of adaptive evolution in bacterial communities. At the same time, the host range of many bacteriophages-and thus one of the selective pressures acting on complex microbial systems in nature-remains poorly characterized. Here, we computationally inferred the putative host ranges of 40 cluster P mycobacteriophages, including members from 6 subclusters (P1-P6). A series of comparative genomic analyses revealed that mycobacteriophages of subcluster P1 are restricted to the Mycobacterium genus, whereas mycobacteriophages of subclusters P2-P6 are likely also able to infect other genera, several of which are commonly associated with human disease. Further genomic analysis highlighted that the majority of cluster P mycobacteriophages harbor a conserved integration-dependent immunity system, hypothesized to be the ancestral state of a genetic switch that controls the shift between lytic and lysogenic life cycles-a temperate characteristic that impedes their usage in antibacterial applications.
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Affiliation(s)
| | | | - Gabriella Cerna
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Tyler Johnston
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Shriya Kakde
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Keith Karuku
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Maria Kowal
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Jasmine Monahan
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Jillian Murray
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Teresa Nguyen
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Aurely Sanchez Carreon
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Abigail Streiff
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Blake Su
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- School of Politics and Global Studies, Arizona State University, Tempe, AZ 85281, USA
| | - Faith Youkhana
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Saige Munig
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Zeel Patel
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Minerva So
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Makena Sy
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Sarah Weiss
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Susanne P Pfeifer
- Corresponding author: Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA.
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Conrad SJ, Raza T, Peterson EA, Liem J, Connor R, Nounamo B, Cannon M, Liu J. Myxoma virus lacking the host range determinant M062 stimulates cGAS-dependent type 1 interferon response and unique transcriptomic changes in human monocytes/macrophages. PLoS Pathog 2022; 18:e1010316. [PMID: 36103568 PMCID: PMC9473615 DOI: 10.1371/journal.ppat.1010316] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 08/04/2022] [Indexed: 11/19/2022] Open
Abstract
The evolutionarily successful poxviruses possess effective and diverse strategies to circumvent or overcome host defense mechanisms. Poxviruses encode many immunoregulatory proteins to evade host immunity to establish a productive infection and have unique means of inhibiting DNA sensing-dependent type 1 interferon (IFN-I) responses, a necessity given their dsDNA genome and exclusively cytoplasmic life cycle. We found that the key DNA sensing inhibition by poxvirus infection was dominant during the early stage of poxvirus infection before DNA replication. In an effort to identify the poxvirus gene products which subdue the antiviral proinflammatory responses (e.g., IFN-I response), we investigated the function of one early gene that is the known host range determinant from the highly conserved poxvirus host range C7L superfamily, myxoma virus (MYXV) M062. Host range factors are unique features of poxviruses that determine the species and cell type tropism. Almost all sequenced mammalian poxviruses retain at least one homologue of the poxvirus host range C7L superfamily. In MYXV, a rabbit-specific poxvirus, the dominant and broad-spectrum host range determinant of the C7L superfamily is the M062R gene. The M062R gene product is essential for MYXV infection in almost all cells tested from different mammalian species and specifically inhibits the function of host Sterile αMotif Domain-containing 9 (SAMD9), as M062R-null (ΔM062R) MYXV causes abortive infection in a SAMD9-dependent manner. In this study we investigated the immunostimulatory property of the ΔM062R. We found that the replication-defective ΔM062R activated host DNA sensing pathway during infection in a cGAS-dependent fashion and that knocking down SAMD9 expression attenuated proinflammatory responses. Moreover, transcriptomic analyses showed a unique feature of the host gene expression landscape that is different from the dsDNA alone-stimulated inflammatory state. This study establishes a link between the anti-neoplastic function of SAMD9 and the regulation of innate immune responses. Poxviruses encode a group of genes called host range determinants to maintain or expand their host tropism. The mechanism by which many viral host range factors function remains elusive. Some host range factors possess immunoregulatory functions responsible for evading or subduing host immune defense mechanisms. Most known immunoregulatory proteins encoded by poxviruses are dispensable for viral replication in vitro. The uniqueness of MYXV M062R is that it is essential for viral infection in vitro and belongs to one of the most conserved poxvirus host range families, the C7L superfamily. There is one known host target of the MYXV M062 protein, SAMD9. SAMD9 is constitutively expressed in mammalian cells and exclusively present in the cytoplasm with an anti-neoplastic function. Humans with deleterious mutations in SAMD9 present disease that ranges from lethality at a young age to a predisposition to myelodysplastic syndromes (MDS) that often require bone marrow transplantation. More importantly, SAMD9 serves as an important antiviral intrinsic molecule to many viruses. The cellular function of SAMD9 remains unclear mostly due to the difficulty of studying this protein, i.e., its large size, long half-life, and its constitutive expression in most cells. In this study we used M062R-null MYXV as a tool to study SAMD9 function and report a functional link between SAMD9 and the regulation of the proinflammatory responses triggered by cGAS-dependent DNA sensing.
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Affiliation(s)
- Steven J. Conrad
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences (UAMS), Little Rock, Arkansas, United States of America
| | - Tahseen Raza
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences (UAMS), Little Rock, Arkansas, United States of America
| | - Erich A. Peterson
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Jason Liem
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Richard Connor
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences (UAMS), Little Rock, Arkansas, United States of America
| | - Bernice Nounamo
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences (UAMS), Little Rock, Arkansas, United States of America
| | - Martin Cannon
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences (UAMS), Little Rock, Arkansas, United States of America
| | - Jia Liu
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences (UAMS), Little Rock, Arkansas, United States of America
- Center of Pathogenesis and Host Inflammatory Responses, University of Arkansas for Medical Sciences (UAMS), Little Rock, Arkansas, United States of America
- * E-mail:
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Cheng RA, Orsi RH, Wiedmann M. The Number and Type of Chaperone-Usher Fimbriae Reflect Phylogenetic Clade Rather than Host Range in Salmonella. mSystems 2022; 7:e0011522. [PMID: 35467401 PMCID: PMC9238391 DOI: 10.1128/msystems.00115-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/03/2022] [Indexed: 01/21/2023] Open
Abstract
Salmonella is one of the most successful foodborne pathogens worldwide, owing in part to its ability to colonize or infect a wide range of hosts. Salmonella serovars are known to encode a variety of different fimbriae (hairlike organelles that facilitate binding to surfaces); however, the distribution, number, and sequence diversity of fimbriae encoded across different lineages of Salmonella were unknown. We queried whole-genome sequence (WGS) data for 242 Salmonella enterica subsp. enterica (subspecies enterica) isolates from the top 217 serovars associated with isolation from humans and agricultural animals; this effort identified 2,894 chaperone-usher (CU)-type fimbrial usher sequences, representing the most conserved component of CU fimbriae. On average, isolates encoded 12 different CU fimbrial ushers (6 to 18 per genome), although the distribution varied significantly (P = 1.328E-08) by phylogenetic clade, with isolates in section Typhi having significantly fewer fimbrial ushers than isolates in clade A2 (medians = 10 and 12 ushers, respectively). Characterization of fimbriae in additional non-enterica subspecies genomes suggested that 8 fimbrial ushers were classified as being unique to subspecies enterica isolates, suggesting that the majority of fimbriae were most likely acquired prior to the divergence of subspecies enterica. Characterization of mobile elements suggested that plasmids represent an important vehicle facilitating the acquisition of a wide range of fimbrial ushers, particularly for the acquisition of fimbriae from other Gram-negative genera. Overall, our results suggest that differences in the number and type of fimbriae encoded most likely reflect differences in phylogenetic clade rather than differences in host range. IMPORTANCE Fimbriae of the CU assembly pathway represent important organelles that mediate Salmonella's interactions with host tissues and abiotic surfaces. Our analyses provide a comprehensive overview of the diversity of CU fimbriae in Salmonella spp., highlighting that the majority of CU fimbriae are distributed broadly across multiple subspecies and suggesting that acquisition most likely occurred prior to the divergence of subspecies enterica. Our data also suggest that plasmids represent the primary vehicles facilitating the horizontal transfer of diverse CU fimbriae in Salmonella. Finally, the observed high sequence similarity between some ushers suggests that different names may have been assigned to closely related fimbrial ushers that likely should be represented by a single designation. This highlights the need to establish standard criteria for fimbria classification and nomenclature, which will also facilitate future studies seeking to associate virulence factors with adaptation to or differences in the likelihood of causing disease in a given host.
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Affiliation(s)
- Rachel A. Cheng
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Renato H. Orsi
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York, USA
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Abstract
Microsporidia are a large phylum of obligate intracellular parasites that infect an extremely diverse range of animals and protists. In this chapter, we review what is currently known about microsporidia host specificity and what factors influence microsporidia infection. Extensive sampling in nature from related hosts has provided insight into the host range of many microsporidia species. These field studies have been supported by experiments conducted in controlled laboratory environments which have helped to demonstrate host specificity. Together, these approaches have revealed that, while examples of generalist species exist, microsporidia specificity is often narrow, and species typically infect one or several closely related hosts. For microsporidia to successfully infect and complete their life cycle within a compatible host, several steps must occur, including spore germination, host cell invasion, and proliferation of the parasite within the host tissue. Many factors influence infection, including temperature, seasonality, nutrient availability, and the presence or absence of microbes, as well as the developmental stage, sex, and genetics of the host. Several studies have identified host genomic regions that influence resistance to microsporidia, and future work is likely to uncover molecular mechanisms of microsporidia host specificity in more detail.
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Affiliation(s)
- Alexandra R Willis
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Aaron W Reinke
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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Wei C, Shan KJ, Wang W, Zhang S, Huan Q, Qian W. Evidence for a mouse origin of the SARS-CoV-2 Omicron variant. J Genet Genomics 2021; 48:1111-1121. [PMID: 34954396 PMCID: PMC8702434 DOI: 10.1016/j.jgg.2021.12.003] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 12/12/2022]
Abstract
The rapid accumulation of mutations in the SARS-CoV-2 Omicron variant that enabled its outbreak raises questions as to whether its proximal origin occurred in humans or another mammalian host. Here, we identified 45 point mutations that Omicron acquired since divergence from the B.1.1 lineage. We found that the Omicron spike protein sequence was subjected to stronger positive selection than that of any reported SARS-CoV-2 variants known to evolve persistently in human hosts, suggesting a possibility of host-jumping. The molecular spectrum of mutations (i.e., the relative frequency of the 12 types of base substitutions) acquired by the progenitor of Omicron was significantly different from the spectrum for viruses that evolved in human patients but resembled the spectra associated with virus evolution in a mouse cellular environment. Furthermore, mutations in the Omicron spike protein significantly overlapped with SARS-CoV-2 mutations known to promote adaptation to mouse hosts, particularly through enhanced spike protein binding affinity for the mouse cell entry receptor. Collectively, our results suggest that the progenitor of Omicron jumped from humans to mice, rapidly accumulated mutations conducive to infecting that host, then jumped back into humans, indicating an inter-species evolutionary trajectory for the Omicron outbreak.
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Affiliation(s)
- Changshuo Wei
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ke-Jia Shan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiguang Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuya Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing Huan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Wenfeng Qian
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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King SB, Singh M. Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections. PLoS Comput Biol 2021; 17:e1009560. [PMID: 34793437 PMCID: PMC8601562 DOI: 10.1371/journal.pcbi.1009560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 10/12/2021] [Indexed: 12/24/2022] Open
Abstract
Severe acute respiratory coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is of zoonotic origin. Evolutionary analyses assessing whether coronaviruses similar to SARS-CoV-2 infected ancestral species of modern-day animal hosts could be useful in identifying additional reservoirs of potentially dangerous coronaviruses. We reasoned that if a clade of species has been repeatedly exposed to a virus, then their proteins relevant for viral entry may exhibit adaptations that affect host susceptibility or response. We perform comparative analyses across the mammalian phylogeny of angiotensin-converting enzyme 2 (ACE2), the cellular receptor for SARS-CoV-2, in order to uncover evidence for selection acting at its binding interface with the SARS-CoV-2 spike protein. We uncover that in rodents there is evidence for adaptive amino acid substitutions at positions comprising the ACE2-spike interaction interface, whereas the variation within ACE2 proteins in primates and some other mammalian clades is not consistent with evolutionary adaptations. We also analyze aminopeptidase N (APN), the receptor for the human coronavirus 229E, a virus that causes the common cold, and find evidence for adaptation in primates. Altogether, our results suggest that the rodent and primate lineages may have had ancient exposures to viruses similar to SARS-CoV-2 and HCoV-229E, respectively.
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Affiliation(s)
- Sean B. King
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Mona Singh
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
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11
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Meekins DA, Gaudreault NN, Richt JA. Natural and Experimental SARS-CoV-2 Infection in Domestic and Wild Animals. Viruses 2021; 13:1993. [PMID: 34696423 PMCID: PMC8540328 DOI: 10.3390/v13101993] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 is the etiological agent responsible for the ongoing COVID-19 pandemic, which continues to spread with devastating effects on global health and socioeconomics. The susceptibility of domestic and wild animal species to infection is a critical facet of SARS-CoV-2 ecology, since reverse zoonotic spillover events resulting in SARS-CoV-2 outbreaks in animal populations could result in the establishment of new virus reservoirs. Adaptive mutations in the virus to new animal species could also complicate ongoing mitigation strategies to combat SARS-CoV-2. In addition, animal species susceptible to SARS-CoV-2 infection are essential as standardized preclinical models for the development and efficacy testing of vaccines and therapeutics. In this review, we summarize the current findings regarding the susceptibility of different domestic and wild animal species to experimental SARS-CoV-2 infection and provide detailed descriptions of the clinical disease and transmissibility in these animals. In addition, we outline the documented natural infections in animals that have occurred at the human-animal interface. A comprehensive understanding of animal susceptibility to SARS-CoV-2 is crucial to inform public health, veterinary, and agricultural systems, and to guide environmental policies.
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Affiliation(s)
- David A. Meekins
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (D.A.M.); (N.N.G.)
- Center of Excellence for Emerging and Zoonotic Animal Diseases (CEEZAD), College of Veterinary Medicine, Kansas State University, Manhattan, KS 66502, USA
| | - Natasha N. Gaudreault
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (D.A.M.); (N.N.G.)
- Center of Excellence for Emerging and Zoonotic Animal Diseases (CEEZAD), College of Veterinary Medicine, Kansas State University, Manhattan, KS 66502, USA
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (D.A.M.); (N.N.G.)
- Center of Excellence for Emerging and Zoonotic Animal Diseases (CEEZAD), College of Veterinary Medicine, Kansas State University, Manhattan, KS 66502, USA
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12
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Knezevic P, Petrovic Fabijan A, Gavric D, Pejic J, Doffkay Z, Rakhely G. Phages from Genus Bruynoghevirus and Phage Therapy: Pseudomonas Phage Delta Case. Viruses 2021; 13:1965. [PMID: 34696396 PMCID: PMC8540360 DOI: 10.3390/v13101965] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 09/23/2021] [Indexed: 11/17/2022] Open
Abstract
The applicability and safety of bacteriophage Delta as a potential anti-Pseudomonas aeruginosa agent belonging to genus Bruynoghevirus (family Podoviridae) was characterised. Phage Delta belongs to the species Pseudomonas virus PaP3, which has been described as a temperate, with cos sites at the end of the genome. The phage Delta possesses a genome of 45,970 bp that encodes tRNA for proline (Pro), aspartic acid (Asp) and asparagine (Asn) and does not encode any known protein involved in lysogeny formation or persistence. Analysis showed that phage Delta has 182 bp direct terminal repeats at the end of genome and lysogeny was confirmed, neither upon infection at low nor at high multiplicity of infection (MOI). The turbid plaques that appear on certain host lawns can result from bacteriophage insensitive mutants that occur with higher frequency (10-4). In silico analysis showed that the genome of Delta phage does not encode any known bacterial toxin or virulence factor, determinants of antibiotic resistance and known human allergens. Based on the broad host range and high lytic activity against planktonic and biofilm cells, phage Delta represents a promising candidate for phage therapy.
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Affiliation(s)
- Petar Knezevic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 3, 21 000 Novi Sad, Serbia; (A.P.F.); (D.G.); (J.P.)
| | - Aleksandra Petrovic Fabijan
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 3, 21 000 Novi Sad, Serbia; (A.P.F.); (D.G.); (J.P.)
| | - Damir Gavric
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 3, 21 000 Novi Sad, Serbia; (A.P.F.); (D.G.); (J.P.)
| | - Jovana Pejic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 3, 21 000 Novi Sad, Serbia; (A.P.F.); (D.G.); (J.P.)
| | - Zsolt Doffkay
- Department of Biotechnology, University of Szeged, Temesvari krt. 62, H-6726 Szeged, Hungary; (Z.D.); (G.R.)
| | - Gábor Rakhely
- Department of Biotechnology, University of Szeged, Temesvari krt. 62, H-6726 Szeged, Hungary; (Z.D.); (G.R.)
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13
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Hafeez M, Li X, Ullah F, Zhang Z, Zhang J, Huang J, Khan MM, Chen L, Ren X, Zhou S, Fernández-Grandon GM, Zalucki MP, Lu Y. Behavioral and Physiological Plasticity Provides Insights into Molecular Based Adaptation Mechanism to Strain Shift in Spodoptera frugiperda. Int J Mol Sci 2021; 22:10284. [PMID: 34638623 PMCID: PMC8508907 DOI: 10.3390/ijms221910284] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/19/2021] [Accepted: 09/21/2021] [Indexed: 12/20/2022] Open
Abstract
How herbivorous insects adapt to host plants is a key question in ecological and evolutionary biology. The fall armyworm, (FAW) Spodoptera frugiperda (J.E. Smith), although polyphagous and a major pest on various crops, has been reported to have a rice and corn (maize) feeding strain in its native range in the Americas. The species is highly invasive and has recently established in China. We compared behavioral changes in larvae and adults of a corn population (Corn) when selected on rice (Rice) and the molecular basis of these adaptational changes in midgut and antennae based on a comparative transcriptome analysis. Larvae of S. frugiperda reared on rice plants continuously for 20 generations exhibited strong feeding preference for with higher larval performance and pupal weight on rice than on maize plants. Similarly, females from the rice selected population laid significantly more eggs on rice as compared to females from maize population. The most highly expressed DEGs were shown in the midgut of Rice vs. Corn. A total of 6430 DEGs were identified between the populations mostly in genes related to digestion and detoxification. These results suggest that potential adaptations for feeding on rice crops, may contribute to the current rapid spread of fall armyworm on rice crops in China and potentially elsewhere. Consistently, highly expressed DEGs were also shown in antennae; a total of 5125 differentially expressed genes (DEGs) s were identified related to the expansions of major chemosensory genes family in Rice compared to the Corn feeding population. These results not only provide valuable insight into the molecular mechanisms in host plants adaptation of S. frugiperda but may provide new gene targets for the management of this pest.
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Affiliation(s)
- Muhammad Hafeez
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (M.H.); (X.L.); (Z.Z.); (J.Z.); (J.H.); (L.C.); (X.R.); (S.Z.)
- State Key Laboratory of Rice Biology, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaowei Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (M.H.); (X.L.); (Z.Z.); (J.Z.); (J.H.); (L.C.); (X.R.); (S.Z.)
| | - Farman Ullah
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China;
| | - Zhijun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (M.H.); (X.L.); (Z.Z.); (J.Z.); (J.H.); (L.C.); (X.R.); (S.Z.)
| | - Jinming Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (M.H.); (X.L.); (Z.Z.); (J.Z.); (J.H.); (L.C.); (X.R.); (S.Z.)
| | - Jun Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (M.H.); (X.L.); (Z.Z.); (J.Z.); (J.H.); (L.C.); (X.R.); (S.Z.)
| | - Muhammad Musa Khan
- Key Laboratory of Bio-Pesticide Innovation and Application, South China Agricultural University, Guangzhou 510642, China;
| | - Limin Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (M.H.); (X.L.); (Z.Z.); (J.Z.); (J.H.); (L.C.); (X.R.); (S.Z.)
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Lab of Biopesticide and Chemical Biology, Ministry of Education & Fujian Province Key Laboratory of Insect Ecology, College of Plant Protection, Fujian Agriculture and Forest University, Fuzhou 350002, China
| | - Xiaoyun Ren
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (M.H.); (X.L.); (Z.Z.); (J.Z.); (J.H.); (L.C.); (X.R.); (S.Z.)
| | - Shuxing Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (M.H.); (X.L.); (Z.Z.); (J.Z.); (J.H.); (L.C.); (X.R.); (S.Z.)
| | | | - Myron P. Zalucki
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4072, Australia;
| | - Yaobin Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (M.H.); (X.L.); (Z.Z.); (J.Z.); (J.H.); (L.C.); (X.R.); (S.Z.)
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Mollentze N, Babayan SA, Streicker DG. Identifying and prioritizing potential human-infecting viruses from their genome sequences. PLoS Biol 2021; 19:e3001390. [PMID: 34582436 PMCID: PMC8478193 DOI: 10.1371/journal.pbio.3001390] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 08/10/2021] [Indexed: 11/18/2022] Open
Abstract
Determining which animal viruses may be capable of infecting humans is currently intractable at the time of their discovery, precluding prioritization of high-risk viruses for early investigation and outbreak preparedness. Given the increasing use of genomics in virus discovery and the otherwise sparse knowledge of the biology of newly discovered viruses, we developed machine learning models that identify candidate zoonoses solely using signatures of host range encoded in viral genomes. Within a dataset of 861 viral species with known zoonotic status, our approach outperformed models based on the phylogenetic relatedness of viruses to known human-infecting viruses (area under the receiver operating characteristic curve [AUC] = 0.773), distinguishing high-risk viruses within families that contain a minority of human-infecting species and identifying putatively undetected or so far unrealized zoonoses. Analyses of the underpinnings of model predictions suggested the existence of generalizable features of viral genomes that are independent of virus taxonomic relationships and that may preadapt viruses to infect humans. Our model reduced a second set of 645 animal-associated viruses that were excluded from training to 272 high and 41 very high-risk candidate zoonoses and showed significantly elevated predicted zoonotic risk in viruses from nonhuman primates, but not other mammalian or avian host groups. A second application showed that our models could have identified Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) as a relatively high-risk coronavirus strain and that this prediction required no prior knowledge of zoonotic Severe Acute Respiratory Syndrome (SARS)-related coronaviruses. Genome-based zoonotic risk assessment provides a rapid, low-cost approach to enable evidence-driven virus surveillance and increases the feasibility of downstream biological and ecological characterization of viruses.
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Affiliation(s)
- Nardus Mollentze
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Simon A. Babayan
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Daniel G. Streicker
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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15
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Mohammadi M, Smith EA, Stanghellini ME, Kaundal R. Insights into the Host Specificity of a New Oomycete Root Pathogen, Pythium brassicum P1: Whole Genome Sequencing and Comparative Analysis Reveals Contracted Regulation of Metabolism, Protein Families, and Distinct Pathogenicity Repertoire. Int J Mol Sci 2021; 22:ijms22169002. [PMID: 34445718 PMCID: PMC8396444 DOI: 10.3390/ijms22169002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 12/14/2022] Open
Abstract
Pythium brassicum P1 Stanghellini, Mohammadi, Förster, and Adaskaveg is an oomycete root pathogen that has recently been characterized. It only attacks plant species belonging to Brassicaceae family, causing root necrosis, stunting, and yield loss. Since P. brassicum P1 is limited in its host range, this prompted us to sequence its whole genome and compare it to those of broad host range Pythium spp. such as P. aphanidermatum and P. ultimum var. ultimum. A genomic DNA library was constructed with a total of 374 million reads. The sequencing data were assembled using SOAPdenovo2, yielding a total genome size of 50.3 Mb contained in 5434 scaffolds, N50 of 30.2 Kb, 61.2% G+C content, and 13,232 putative protein-coding genes. Pythium brassicum P1 had 175 species-specific gene families, which is slightly below the normal average. Like P. ultimum, P. brassicum P1 genome did not encode any classical RxLR effectors or cutinases, suggesting a significant difference in virulence mechanisms compared to other oomycetes. Pythium brassicum P1 had a much smaller proportions of the YxSL sequence motif in both secreted and non-secreted proteins, relative to other Pythium species. Similarly, P. brassicum P1 had the fewest Crinkler (CRN) effectors of all the Pythium species. There were 633 proteins predicted to be secreted in the P. brassicum P1 genome, which is, again, slightly below average among Pythium genomes. Pythium brassicum P1 had only one cadherin gene with calcium ion-binding LDRE and DxND motifs, compared to Pythium ultimum having four copies. Pythium brassicum P1 had a reduced number of proteins falling under carbohydrate binding module and hydrolytic enzymes. Pythium brassicum P1 had a reduced complement of cellulase and pectinase genes in contrast to P. ultimum and was deficient in xylan degrading enzymes. The contraction in ABC transporter families in P. brassicum P1 is suggested to be the result of a lack of diversity in nutrient uptake and therefore host range.
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Affiliation(s)
- Mojtaba Mohammadi
- Department of Microbiology and Plant Pathology, University of California, 900 University Ave., Riverside, CA 92521, USA; (M.M.); (E.A.S.); (M.E.S.)
| | - Eric A. Smith
- Department of Microbiology and Plant Pathology, University of California, 900 University Ave., Riverside, CA 92521, USA; (M.M.); (E.A.S.); (M.E.S.)
| | - Michael E. Stanghellini
- Department of Microbiology and Plant Pathology, University of California, 900 University Ave., Riverside, CA 92521, USA; (M.M.); (E.A.S.); (M.E.S.)
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, 4820 Old Main Hill, Logan, UT 84322, USA
- Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, 4700 Old Main Hill, Logan, UT 84322, USA
- Correspondence: ; Tel.: +1-(435)-797-4117; Fax: +1-(435)-797-2766
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Hily JM, Poulicard N, Kubina J, Reynard JS, Spilmont AS, Fuchs M, Lemaire O, Vigne E. Metagenomic analysis of nepoviruses: diversity, evolution and identification of a genome region in members of subgroup A that appears to be important for host range. Arch Virol 2021; 166:2789-2801. [PMID: 34370094 PMCID: PMC8421298 DOI: 10.1007/s00705-021-05111-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/01/2021] [Indexed: 11/26/2022]
Abstract
Data mining and metagenomic analysis of 277 open reading frame sequences of bipartite RNA viruses of the genus Nepovirus, family Secoviridae, were performed, documenting how challenging it can be to unequivocally assign a virus to a particular species, especially those in subgroups A and C, based on some of the currently adopted taxonomic demarcation criteria. This work suggests a possible need for their amendment to accommodate pangenome information. In addition, we revealed a host-dependent structure of arabis mosaic virus (ArMV) populations at a cladistic level and confirmed a phylogeographic structure of grapevine fanleaf virus (GFLV) populations. We also identified new putative recombination events in members of subgroups A, B and C. The evolutionary specificity of some capsid regions of ArMV and GFLV that were described previously and biologically validated as determinants of nematode transmission was circumscribed in silico. Furthermore, a C-terminal segment of the RNA-dependent RNA polymerase of members of subgroup A was predicted to be a putative host range determinant based on statistically supported higher π (substitutions per site) values for GFLV and ArMV isolates infecting Vitis spp. compared with non-Vitis-infecting ArMV isolates. This study illustrates how sequence information obtained via high-throughput sequencing can increase our understanding of mechanisms that modulate virus diversity and evolution and create new opportunities for advancing studies on the biology of economically important plant viruses.
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Affiliation(s)
- J M Hily
- IFV, Le Grau-Du-Roi, France.
- Université de Strasbourg, INRAE, SVQV, UMR-A 1131, F-68000, Colmar, France.
| | - N Poulicard
- PHIM, Université Montpellier, IRD, INRAE, Cirad, SupAgro, Montpellier, France
| | - J Kubina
- Université de Strasbourg, INRAE, SVQV, UMR-A 1131, F-68000, Colmar, France
| | - J S Reynard
- Institute for Plant Production Science, Agroscope, 1260, Nyon, Switzerland
| | | | - M Fuchs
- Cornell University, Geneva, NY, USA
| | - O Lemaire
- Université de Strasbourg, INRAE, SVQV, UMR-A 1131, F-68000, Colmar, France
| | - E Vigne
- Université de Strasbourg, INRAE, SVQV, UMR-A 1131, F-68000, Colmar, France.
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Slobodníková L, Markusková B, Kajsík M, Andrezál M, Straka M, Liptáková A, Drahovská H. Characterization of Anti-Bacterial Effect of the Two New Phages against Uropathogenic Escherichia coli. Viruses 2021; 13:v13071348. [PMID: 34372554 PMCID: PMC8310266 DOI: 10.3390/v13071348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/24/2021] [Accepted: 07/09/2021] [Indexed: 12/02/2022] Open
Abstract
Urinary tract infections (UTIs) are among the events that most frequently need medical intervention. Uropathogenic Escherichia coli are frequently their causative agents and the infections are sometimes complicated by the presence of polyresistant nosocomial strains. Phage therapy is a tool that has good prospects for the treatment of these infections. In the present study, we isolated and characterized two bacteriophages with broad host specificity against a panel of local uropathogenic E. coli strains and combined them into a phage cocktail. According to genome sequencing, these phages were closely related and belonged to the Tequatrovirus genus. The newly isolated phages showed very good activity on a panel of local clinical E. coli strains from urinary tract infections. In the form of a two-phage cocktail, they were active on E. coli strains belonging to phylogroups B2 and D, with relatively lower activity in B1 and no response in phylogroup A. Our study is a preliminary step toward the establishment of a national phage bank containing local, well-characterized phages with therapeutic potential for patients in Slovakia.
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Affiliation(s)
- Lívia Slobodníková
- Medical Faculty, Institute of Microbiolog, Comenius University in Bratislava, 81108 Bratislava, Slovakia; (L.S.); (M.S.)
| | - Barbora Markusková
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84104 Bratislava, Slovakia; (B.M.); (M.K.); (M.A.); (H.D.)
| | - Michal Kajsík
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84104 Bratislava, Slovakia; (B.M.); (M.K.); (M.A.); (H.D.)
- Comenius University Science Park, Ilkovičova 8, 84104 Bratislava, Slovakia
| | - Michal Andrezál
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84104 Bratislava, Slovakia; (B.M.); (M.K.); (M.A.); (H.D.)
| | - Marek Straka
- Medical Faculty, Institute of Microbiolog, Comenius University in Bratislava, 81108 Bratislava, Slovakia; (L.S.); (M.S.)
| | - Adriána Liptáková
- Medical Faculty, Institute of Microbiolog, Comenius University in Bratislava, 81108 Bratislava, Slovakia; (L.S.); (M.S.)
- Correspondence:
| | - Hana Drahovská
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84104 Bratislava, Slovakia; (B.M.); (M.K.); (M.A.); (H.D.)
- Comenius University Science Park, Ilkovičova 8, 84104 Bratislava, Slovakia
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18
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Noroy C, Meyer DF. The super repertoire of type IV effectors in the pangenome of Ehrlichia spp. provides insights into host-specificity and pathogenesis. PLoS Comput Biol 2021; 17:e1008788. [PMID: 34252087 PMCID: PMC8274917 DOI: 10.1371/journal.pcbi.1008788] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/26/2021] [Indexed: 11/28/2022] Open
Abstract
The identification of bacterial effectors is essential to understand how obligatory intracellular bacteria such as Ehrlichia spp. manipulate the host cell for survival and replication. Infection of mammals–including humans–by the intracellular pathogenic bacteria Ehrlichia spp. depends largely on the injection of virulence proteins that hijack host cell processes. Several hypothetical virulence proteins have been identified in Ehrlichia spp., but one so far has been experimentally shown to translocate into host cells via the type IV secretion system. However, the current challenge is to identify most of the type IV effectors (T4Es) to fully understand their role in Ehrlichia spp. virulence and host adaptation. Here, we predict the T4E repertoires of four sequenced Ehrlichia spp. and four other Anaplasmataceae as comparative models (pathogenic Anaplasma spp. and Wolbachia endosymbiont) using previously developed S4TE 2.0 software. This analysis identified 579 predicted T4Es (228 pT4Es for Ehrlichia spp. only). The effector repertoires of Ehrlichia spp. overlapped, thereby defining a conserved core effectome of 92 predicted effectors shared by all strains. In addition, 69 species-specific T4Es were predicted with non-canonical GC% mostly in gene sparse regions of the genomes and we observed a bias in pT4Es according to host-specificity. We also identified new protein domain combinations, suggesting novel effector functions. This work presenting the predicted effector collection of Ehrlichia spp. can serve as a guide for future functional characterisation of effectors and design of alternative control strategies against these bacteria. A fundamental step for the survival and replication of intravacuolar bacterial pathogens is the establishment of a replicative niche inside host cells by the secretion of bacterial effector proteins in the cytoplasm of the infected cells. These effectors manipulate host signaling pathways, thus allowing to escape the host degradative pathway and uptake nutrients required for intracellular replication of bacteria. In this study, we used S4TE2.0 software for high-throughput computational prediction of bacterial type IV effectors in zoonotic bacteria of the Anaplasmataceae family. The analysis of protein architecture of effectors helped us to identify the cellular pathways targeted during the infection process. The demonstration that effectors are modular components with a broad variety of protein architectures nicely explains their pleotropic mode of action and enlightens their function. We showed that bacterial adaptation to a given host during evolution requires a minimal repertoire of candidate effectors although further experimental determination is needed. T4Es are of increasing interest for basic research, including comprehension of hijacked cellular pathways, manipulated innate immunity, and application for therapeutics. Indeed pathogenomics-driven studies, especially on genetically intractable intracellular bacteria such as Anaplasmataceae, have now a substantial impact for the development of host-targeted antimicrobials, as an alternative to antibiotics.
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Affiliation(s)
- Christophe Noroy
- CIRAD, UMR ASTRE, Petit-Bourg, Guadeloupe, France
- ASTRE, CIRAD, INRA, Univ Montpellier, Montpellier, France
- Université des Antilles, Fouillole, Pointe-à-Pitre, Guadeloupe, France
| | - Damien F. Meyer
- CIRAD, UMR ASTRE, Petit-Bourg, Guadeloupe, France
- ASTRE, CIRAD, INRA, Univ Montpellier, Montpellier, France
- * E-mail:
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19
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Haque A, Islam S, Bari A, Hossain A, Athanassiou CG, Hasan M. Cold storage-mediated rearing of Trichogramma evanescens Westwood on eggs of Plodia interpunctella (Hübner) and Galleria mellonella L. PLoS One 2021; 16:e0253287. [PMID: 34125871 PMCID: PMC8202947 DOI: 10.1371/journal.pone.0253287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 06/01/2021] [Indexed: 01/27/2023] Open
Abstract
The egg parasitoid Trichogramma evanescens Westwood is considered as an efficient biological control agent for managing several lepidopteran pests and it is widely distributed throughout the world. Mass rearing protocols of parasitoids that are currently in use in biocontrol programs require a meticulous quality control plan, in order to optimize their efficacy, but also their progeny production capacity. In this paper, the effect of different factors on the quality control in mass rearing of T. evenescens, using Plodia interpunctella (Hübner) and Galleria mellonella L. as host species, were investigated. The impact of egg agewas significant in the rates of parasitism, for both host species tested. Significantly highest percent of parasitoid emergence was noticed in two day-old eggs for both host species, while one day-old eggs day exhibited the maximum emergence when both species were used togetherin the same trials. Age-dependent storage egg preservation at either 4 or 9°C significantly influenced the parasitism percentages on both species. The highest parasitism percentage was recorded in two day-old G. mellonella eggs that are kept for 15 days at 9°C while the lower in one day-old P. interpunctella eggs for 60 d storage. Moreover, the highest parasitoid mortality was recorded in T. evanescens reared either on P. interpunctella or G. mellonella at 20°C. Rearing of the parasitoid on a mixture of eggs of both host species resulted in higher parasitism, but not always in higher rates of parasitoid emergence. The results of the present work provide useful information that can be further utilized in rearing protocols of T. evanescens.
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Affiliation(s)
- Aslam Haque
- Department of Crop Science and Technology, Rajshahi University, Rajshahi, Bangladesh
| | - Saiful Islam
- Department of Crop Science and Technology, Rajshahi University, Rajshahi, Bangladesh
| | - Abdul Bari
- Insect Biotechnology Division, Institute of Food and Radiation Biology, Atomic Energy Research Establishment, Savar, Dhaka, Bangladesh
| | - Akhtar Hossain
- Department of Zoology, Rajshahi University, Rajshahi, Bangladesh
| | - Christos G. Athanassiou
- Laboratory of Entomology and Agricultural Zoology, Department of Agriculture, Crop Production and Rural Environment, University of Thessaly, N. Ionia Magnesia, Greece
| | - Mahbub Hasan
- Department of Zoology, Rajshahi University, Rajshahi, Bangladesh
- * E-mail:
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Price JA, Coyne D, Blok VC, Jones JT. Potato cyst nematodes Globodera rostochiensis and G. pallida. Mol Plant Pathol 2021; 22:495-507. [PMID: 33709540 PMCID: PMC8035638 DOI: 10.1111/mpp.13047] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/02/2021] [Accepted: 02/02/2021] [Indexed: 05/12/2023]
Abstract
TAXONOMY Phylum Nematoda; class Chromadorea; order Rhabditida; suborder Tylenchina; infraorder Tylenchomorpha; superfamily Tylenchoidea; family Heteroderidae; subfamily Heteroderinae; Genus Globodera. BIOLOGY Potato cyst nematodes (PCN) are biotrophic, sedentary endoparasitic nematodes. Invasive (second) stage juveniles (J2) hatch from eggs in response to the presence of host root exudates and subsequently locate and invade the host. The nematodes induce the formation of a large, multinucleate syncytium in host roots, formed by fusion of up to 300 root cell protoplasts. The nematodes rely on this single syncytium for the nutrients required to develop through a further three moults to the adult male or female stage. This extended period of biotrophy-between 4 and 6 weeks in total-is almost unparalleled in plant-pathogen interactions. Females remain at the root while adult males revert to the vermiform body plan of the J2 and leave the root to locate and fertilize the female nematodes. The female body forms a cyst that contains the next generation of eggs. HOST RANGE The host range of PCN is limited to plants of the Solanaceae family. While the most economically important hosts are potato (Solanum tuberosum), tomato (Solanum lycopersicum), and aubergine (Solanum melongena), over 170 species of Solanaceae are thought to be potential hosts for PCN (Sullivan et al., 2007). DISEASE SYMPTOMS Symptoms are similar to those associated with nutrient deficiency, such as stunted growth, yellowing of leaves and reduced yields. This absence of specific symptoms reduces awareness of the disease among growers. DISEASE CONTROL Resistance genes (where available in suitable cultivars), application of nematicides, crop rotation. Great effort is put into reducing the spread of PCN through quarantine measures and use of certified seed stocks. USEFUL WEBSITES Genomic information for PCN is accessible through WormBase ParaSite.
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Affiliation(s)
- James A. Price
- School of BiologyBiomedical Sciences Research ComplexUniversity of St AndrewsSt AndrewsUK
- Cell & Molecular Sciences DepartmentThe James Hutton InstituteDundeeUK
| | - Danny Coyne
- International Institute of Tropical Agriculture (IITA)NairobiKenya
| | - Vivian C. Blok
- Cell & Molecular Sciences DepartmentThe James Hutton InstituteDundeeUK
| | - John T. Jones
- School of BiologyBiomedical Sciences Research ComplexUniversity of St AndrewsSt AndrewsUK
- Cell & Molecular Sciences DepartmentThe James Hutton InstituteDundeeUK
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21
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Abstract
Identifying the animal reservoirs from which zoonotic viruses will likely emerge is central to understanding the determinants of disease emergence. Accordingly, there has been an increase in studies attempting zoonotic “risk assessment.” Herein, we demonstrate that the virological data on which these analyses are conducted are incomplete, biased, and rapidly changing with ongoing virus discovery. Together, these shortcomings suggest that attempts to assess zoonotic risk using available virological data are likely to be inaccurate and largely only identify those host taxa that have been studied most extensively. We suggest that virus surveillance at the human–animal interface may be more productive. Determining which organisms harbour viruses that could potentially infect humans is of great topical interest. This Essay demonstrates that the data on which such zoonotic risk assessments are conducted are incomplete, biased, and rapidly changing with ongoing virus discovery.
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Affiliation(s)
- Michelle Wille
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia
- * E-mail:
| | - Jemma L. Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia
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22
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Mou H, Quinlan BD, Peng H, Liu G, Guo Y, Peng S, Zhang L, Davis-Gardner ME, Gardner MR, Crynen G, DeVaux LB, Voo ZX, Bailey CC, Alpert MD, Rader C, Gack MU, Choe H, Farzan M. Mutations derived from horseshoe bat ACE2 orthologs enhance ACE2-Fc neutralization of SARS-CoV-2. PLoS Pathog 2021; 17:e1009501. [PMID: 33836016 PMCID: PMC8059821 DOI: 10.1371/journal.ppat.1009501] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 04/21/2021] [Accepted: 03/24/2021] [Indexed: 01/14/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein mediates infection of cells expressing angiotensin-converting enzyme 2 (ACE2). ACE2 is also the viral receptor of SARS-CoV (SARS-CoV-1), a related coronavirus that emerged in 2002–2003. Horseshoe bats (genus Rhinolophus) are presumed to be the original reservoir of both viruses, and a SARS-like coronavirus, RaTG13, closely related to SARS-CoV-2, has been identified in one horseshoe-bat species. Here we characterize the ability of the S-protein receptor-binding domains (RBDs) of SARS-CoV-1, SARS-CoV-2, pangolin coronavirus (PgCoV), RaTG13, and LyRa11, a bat virus similar to SARS-CoV-1, to bind a range of ACE2 orthologs. We observed that the PgCoV RBD bound human ACE2 at least as efficiently as the SARS-CoV-2 RBD, and that both RBDs bound pangolin ACE2 efficiently. We also observed a high level of variability in binding to closely related horseshoe-bat ACE2 orthologs consistent with the heterogeneity of their RBD-binding regions. However five consensus horseshoe-bat ACE2 residues enhanced ACE2 binding to the SARS-CoV-2 RBD and neutralization of SARS-CoV-2 pseudoviruses by an enzymatically inactive immunoadhesin form of human ACE2 (hACE2-NN-Fc). Two of these mutations impaired neutralization of SARS-CoV-1 pseudoviruses. An hACE2-NN-Fc variant bearing all five mutations neutralized both SARS-CoV-2 pseudovirus and infectious virus more efficiently than wild-type hACE2-NN-Fc. These data suggest that SARS-CoV-1 and -2 originate from distinct bat species, and identify a more potently neutralizing form of soluble ACE2. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), like the closely related virus SARS-CoV (SARS-CoV-1), infects cells by interacting with the cellular receptor angiotensin-converting enzyme 2 (ACE2). This interaction is mediated by the viral spike (S) protein through an independently folded subdomain, described as its receptor-binding domain (RBD). The susceptibility of a species to SARS-CoV-1 or -2 infection correlates with the binding affinity of their respective RBD for the ACE2 orthologs of that species. We therefore investigated the binding affinity of the RBD regions of multiple SARS-like coronaviruses with a range of ACE2 orthologs. Our results are consistent with the hypothesis that pangolins serve as an intermediate between humans and horseshoe bats. We further observed a high level of variability in the ability of the SARS-CoV-2 RBD to bind horseshoe bat ACE2 orthologs, suggesting ongoing selection pressure on their receptor ACE2 proteins from SARS-like viruses. Indeed, mutations derived from different horseshoe bat orthologs introduced into a soluble form of human ACE2 differentially impacted SARS-CoV-1 and SARS-CoV-2 S-protein-mediated infection. A combination of five residues present in multiple horseshoe bats increased the ability of a soluble form of ACE2 to neutralize SARS-CoV-2 S-protein-mediated infection. Thus horseshoe bats ACE2 orthologs can provide insight useful to improving the potency of ACE2-based therapeutics.
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Affiliation(s)
- Huihui Mou
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America
| | - Brian D. Quinlan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America
| | - Haiyong Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America
| | - Guanqun Liu
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, United States of America
| | - Yan Guo
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America
| | - Shoujiao Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America
| | - Lizhou Zhang
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America
| | - Meredith E. Davis-Gardner
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America
| | - Matthew R. Gardner
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America
| | - Gogce Crynen
- Bioinformatics and Statistics Core, The Scripps Research Institute, Jupiter, FL, United States of America
| | - Lindsey B. DeVaux
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America
| | - Zhi Xiang Voo
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America
| | | | | | - Christoph Rader
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America
- * E-mail: (CR); (MUG); (HC); (MF)
| | - Michaela U. Gack
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, United States of America
- * E-mail: (CR); (MUG); (HC); (MF)
| | - Hyeryun Choe
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America
- * E-mail: (CR); (MUG); (HC); (MF)
| | - Michael Farzan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America
- * E-mail: (CR); (MUG); (HC); (MF)
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23
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Abstract
Rickettsiae are obligate intracellular bacteria that can cause life-threatening illnesses and are among the oldest known vector-borne pathogens. Members of this genus are extraordinarily diverse and exhibit a broad host range. To establish intracellular infection, Rickettsia species undergo complex, multistep life cycles that are encoded by heavily streamlined genomes. As a result of reductive genome evolution, rickettsiae are exquisitely tailored to their host cell environment but cannot survive extracellularly. This host-cell dependence makes for a compelling system to uncover novel host-pathogen biology, but it has also hindered experimental progress. Consequently, the molecular details of rickettsial biology and pathogenesis remain poorly understood. With recent advances in molecular biology and genetics, the field is poised to start unraveling the molecular mechanisms of these host-pathogen interactions. Here, we review recent discoveries that have shed light on key aspects of rickettsial biology. These studies have revealed that rickettsiae subvert host cells using mechanisms that are distinct from other better-studied pathogens, underscoring the great potential of the Rickettsia genus for revealing novel biology. We also highlight several open questions as promising areas for future study and discuss the path toward solving the fundamental mysteries of this neglected and emerging human pathogen.
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Affiliation(s)
- Jon McGinn
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Rebecca L Lamason
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
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24
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Cohen E, Azriel S, Auster O, Gal A, Zitronblat C, Mikhlin S, Scharte F, Hensel M, Rahav G, Gal-Mor O. Pathoadaptation of the passerine-associated Salmonella enterica serovar Typhimurium lineage to the avian host. PLoS Pathog 2021; 17:e1009451. [PMID: 33739988 PMCID: PMC8011750 DOI: 10.1371/journal.ppat.1009451] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/31/2021] [Accepted: 03/04/2021] [Indexed: 12/15/2022] Open
Abstract
Salmonella enterica is a diverse bacterial pathogen and a primary cause of human and animal infections. While many S. enterica serovars present a broad host-specificity, several specialized pathotypes have been adapted to colonize and cause disease in one or limited numbers of host species. The underlying mechanisms defining Salmonella host-specificity are far from understood. Here, we present genetic analysis, phenotypic characterization and virulence profiling of a monophasic S. enterica serovar Typhimurium strain that was isolated from several wild sparrows in Israel. Whole genome sequencing and complete assembly of its genome demonstrate a unique genetic signature that includes the integration of the BTP1 prophage, loss of the virulence plasmid, pSLT and pseudogene accumulation in multiple T3SS-2 effectors (sseJ, steC, gogB, sseK2, and sseK3), catalase (katE), tetrathionate respiration (ttrB) and several adhesion/ colonization factors (lpfD, fimH, bigA, ratB, siiC and siiE) encoded genes. Correspondingly, this strain demonstrates impaired biofilm formation, intolerance to oxidative stress and compromised intracellular replication within non-phagocytic host cells. Moreover, while this strain showed attenuated pathogenicity in the mouse, it was highly virulent and caused an inflammatory disease in an avian host. Overall, our findings demonstrate a unique phenotypic profile and genetic makeup of an overlooked S. Typhimurium sparrow-associated lineage and present distinct genetic signatures that are likely to contribute to its pathoadaptation to passerine birds. During Salmonella enterica evolution, many different ecological niches have been effectively occupied by this highly diverse bacterial pathogen. While many S. enterica serovars successfully maintained their ability to infect and colonize in a wide-array of host species, a few biotypes have evolved to colonize and cause a disease in only one or a small group of hosts. The evolutionary dynamic and the mechanisms shaping the host-specificity of Salmonella adapted strains are important to better understand Salmonella pathogenicity and its ecology, but still not fully understood. Here, we report genetic and phenotypic characterization of a S. Typhimurium strain that was isolated from several wild sparrows in Israel. This strain presented unique phenotypic profile that included impaired biofilm formation, high sensitivity to oxidative stress and reduced intracellular replication in non-phagocytic cells. In addition, while this strain was able to cause high inflammatory disease in an avian host, it was highly attenuated in the mouse model. Genome analysis identified that specific genetic signatures found in the sparrow strain are more frequently associated with poultry isolates than clinical isolates of S. Typhimurium. These genetic features are expected to accumulatively contribute toward the adaptation of this strain to birds.
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Affiliation(s)
- Emiliano Cohen
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | - Shalevet Azriel
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | - Oren Auster
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Clinical Microbiology and Immunology, Tel Aviv University, Tel Aviv, Israel
| | - Adiv Gal
- Faculty of Sciences, Kibbutzim College, Tel-Aviv Israel
| | | | | | - Felix Scharte
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Michael Hensel
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Galia Rahav
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ohad Gal-Mor
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Clinical Microbiology and Immunology, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
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25
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Naz S, Dabral S, Nagarajan SN, Arora D, Singh LV, Kumar P, Singh Y, Kumar D, Varshney U, Nandicoori VK. Compromised base excision repair pathway in Mycobacterium tuberculosis imparts superior adaptability in the host. PLoS Pathog 2021; 17:e1009452. [PMID: 33740020 PMCID: PMC8011731 DOI: 10.1371/journal.ppat.1009452] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 03/31/2021] [Accepted: 03/04/2021] [Indexed: 11/28/2022] Open
Abstract
Tuberculosis caused by Mycobacterium tuberculosis (Mtb) is a significant public health concern, exacerbated by the emergence of drug-resistant TB. To combat the host’s dynamic environment, Mtb encodes multiple DNA repair enzymes that play a critical role in maintaining genomic integrity. Mtb possesses a GC-rich genome, rendering it highly susceptible to cytosine deaminations, resulting in the occurrence of uracils in the DNA. UDGs encoded by ung and udgB initiate the repair; hence we investigated the biological impact of deleting UDGs in the adaptation of pathogen. We generated gene replacement mutants of uracil DNA glycosylases, individually (RvΔung, RvΔudgB) or together (RvΔdKO). The double KO mutant, RvΔdKO exhibited remarkably higher spontaneous mutation rate, in the presence of antibiotics. Interestingly, RvΔdKO showed higher survival rates in guinea pigs and accumulated large number of SNPs as revealed by whole-genome sequence analysis. Competition assays revealed the superior fitness of RvΔdKO over Rv, both in ex vivo and in vivo conditions. We propose that compromised DNA repair results in the accumulation of mutations, and a subset of these drives adaptation in the host. Importantly, this property allowed us to utilize RvΔdKO for the facile identification of drug targets. Mutation in the genome of bacteria contributes to the acquisition of drug resistance. Mutations in bacteria can arise due to exposures to antibiotics, oxidative, reductive, and many other stresses that bacteria encounter in the host. Mtb has multiple DNA repair mechanisms, including a base excision repair pathway to restore the damaged genome. Here we set out to determine the impact of deleting the Uracil DNA base excision pathway on pathogen adaptability to both antibiotic and host induced stresses. Combinatorial mutant of Mtb UDGs showed higher spontaneous rates of mutations when subjected to antibiotic stress and showed higher survival levels in the guinea pig model of infection. Whole-genome sequence analysis showed significant accumulation of SNPs, suggesting that mutations providing survival advantage may have been positively selected. We also showed that double mutant of Mtb UDGs would be an excellent means to identify antibiotic targets in the bacteria. Competition experiments wherein we pitted wild type and double mutant against each other demonstrated that double mutant has a decisive edge over the wild type. Together, data suggest that the absence of a base excision repair pathway leads to higher mutations and provides a survival advantage under stress. They could be an invaluable tool for identifying targets of new antibiotics.
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Affiliation(s)
- Saba Naz
- Signal Transduction Lab, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
- Department of Zoology, University of Delhi, Delhi, India
| | - Shruti Dabral
- Cellular Immunology Group, International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | | | - Divya Arora
- Signal Transduction Lab, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Lakshya Veer Singh
- Cellular Immunology Group, International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Pradeep Kumar
- Department of Microbiology & Cell Biology, Indian Institute of Sciences, Bangalore, India
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, India
| | - Dhiraj Kumar
- Cellular Immunology Group, International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Umesh Varshney
- Department of Microbiology & Cell Biology, Indian Institute of Sciences, Bangalore, India
- * E-mail: (UV); (VKN)
| | - Vinay Kumar Nandicoori
- Signal Transduction Lab, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
- * E-mail: (UV); (VKN)
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26
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Devaux CA, Pinault L, Osman IO, Raoult D. Can ACE2 Receptor Polymorphism Predict Species Susceptibility to SARS-CoV-2? Front Public Health 2021; 8:608765. [PMID: 33643982 PMCID: PMC7902720 DOI: 10.3389/fpubh.2020.608765] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/23/2020] [Indexed: 12/16/2022] Open
Abstract
A novel severe acute respiratory syndrome coronavirus, SARS-CoV-2, emerged in China in December 2019 and spread worldwide, causing more than 1.3 million deaths in 11 months. Similar to the human SARS-CoV, SARS-CoV-2 shares strong sequence homologies with a sarbecovirus circulating in Rhinolophus affinis bats. Because bats are expected to be able to transmit their coronaviruses to intermediate animal hosts that in turn are a source of viruses able to cross species barriers and infect humans (so-called spillover model), the identification of an intermediate animal reservoir was the subject of intense researches. It was claimed that a reptile (Ophiophagus hannah) was the intermediate host. This hypothesis was quickly ruled out and replaced by the pangolin (Manis javanica) hypothesis. Yet, pangolin was also recently exonerated from SARS-CoV-2 transmission to humans, leaving other animal species as presumed guilty. Guided by the spillover model, several laboratories investigated in silico the species polymorphism of the angiotensin I converting enzyme 2 (ACE2) to find the best fits with the SARS-CoV-2 spike receptor-binding site. Following the same strategy, we used multi-sequence alignment, 3-D structure analysis, and electrostatic potential surface generation of ACE2 variants to predict their binding capacity to SARS-CoV-2. We report evidence that such simple in silico investigation is a powerful tool to quickly screen which species are potentially susceptible to SARS-CoV-2. However, possible receptor binding does not necessarily lead to successful replication in host. Therefore, we also discuss here the limitations of these in silico approaches in our quest on the origins of COVID-19 pandemic.
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Affiliation(s)
- Christian A. Devaux
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU–Méditerranée Infection, Marseille, France
- CNRS, Marseille, France
| | - Lucile Pinault
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU–Méditerranée Infection, Marseille, France
| | - Ikram Omar Osman
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU–Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU–Méditerranée Infection, Marseille, France
- Fondation IHU–Méditerranée Infection, Marseille, France
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Bergner LM, Orton RJ, Broos A, Tello C, Becker DJ, Carrera JE, Patel AH, Biek R, Streicker DG. Diversification of mammalian deltaviruses by host shifting. Proc Natl Acad Sci U S A 2021; 118:e2019907118. [PMID: 33397804 PMCID: PMC7826387 DOI: 10.1073/pnas.2019907118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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] [Indexed: 02/06/2023] Open
Abstract
Hepatitis delta virus (HDV) is an unusual RNA agent that replicates using host machinery but exploits hepatitis B virus (HBV) to mobilize its spread within and between hosts. In doing so, HDV enhances the virulence of HBV. How this seemingly improbable hyperparasitic lifestyle emerged is unknown, but it underpins the likelihood that HDV and related deltaviruses may alter other host-virus interactions. Here, we show that deltaviruses diversify by transmitting between mammalian species. Among 96,695 RNA sequence datasets, deltaviruses infected bats, rodents, and an artiodactyl from the Americas but were absent from geographically overrepresented Old World representatives of each mammalian order, suggesting a relatively recent diversification within the Americas. Consistent with diversification by host shifting, both bat and rodent-infecting deltaviruses were paraphyletic, and coevolutionary modeling rejected cospeciation with mammalian hosts. In addition, a 2-y field study showed common vampire bats in Peru were infected by two divergent deltaviruses, indicating multiple introductions to a single host species. One vampire bat-associated deltavirus was detected in the saliva of up to 35% of individuals, formed phylogeographically compartmentalized clades, and infected a sympatric bat, illustrating horizontal transmission within and between species on ecological timescales. Consistent absence of HBV-like viruses in two deltavirus-infected bat species indicated acquisitions of novel viral associations during the divergence of bat and human-infecting deltaviruses. Our analyses support an American zoonotic origin of HDV and reveal prospects for future cross-species emergence of deltaviruses. Given their peculiar life history, deltavirus host shifts will have different constraints and disease outcomes compared to ordinary animal pathogens.
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Affiliation(s)
- Laura M Bergner
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland;
- Medical Research Center-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland
| | - Richard J Orton
- Medical Research Center-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland
| | - Alice Broos
- Medical Research Center-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland
| | - Carlos Tello
- Association for the Conservation and Development of Natural Resources, 15037 Lima, Perú
- Yunkawasi, 15049 Lima, Perú
| | - Daniel J Becker
- Department of Biology, University of Oklahoma, Norman, OK 73019
| | - Jorge E Carrera
- Departamento de Mastozoología, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima 15081, Perú
- Programa de Conservación de Murciélagos de Perú, Piura 20001, Perú
| | - Arvind H Patel
- Medical Research Center-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland
| | - Daniel G Streicker
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland;
- Medical Research Center-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland
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Boeckaerts D, Stock M, Criel B, Gerstmans H, De Baets B, Briers Y. Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins. Sci Rep 2021; 11:1467. [PMID: 33446856 PMCID: PMC7809048 DOI: 10.1038/s41598-021-81063-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 12/30/2020] [Indexed: 12/04/2022] Open
Abstract
Nowadays, bacteriophages are increasingly considered as an alternative treatment for a variety of bacterial infections in cases where classical antibiotics have become ineffective. However, characterizing the host specificity of phages remains a labor- and time-intensive process. In order to alleviate this burden, we have developed a new machine-learning-based pipeline to predict bacteriophage hosts based on annotated receptor-binding protein (RBP) sequence data. We focus on predicting bacterial hosts from the ESKAPE group, Escherichia coli, Salmonella enterica and Clostridium difficile. We compare the performance of our predictive model with that of the widely used Basic Local Alignment Search Tool (BLAST). Our best-performing predictive model reaches Precision-Recall Area Under the Curve (PR-AUC) scores between 73.6 and 93.8% for different levels of sequence similarity in the collected data. Our model reaches a performance comparable to that of BLASTp when sequence similarity in the data is high and starts outperforming BLASTp when sequence similarity drops below 75%. Therefore, our machine learning methods can be especially useful in settings in which sequence similarity to other known sequences is low. Predicting the hosts of novel metagenomic RBP sequences could extend our toolbox to tune the host spectrum of phages or phage tail-like bacteriocins by swapping RBPs.
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Affiliation(s)
- Dimitri Boeckaerts
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Michiel Stock
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Bjorn Criel
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Hans Gerstmans
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
- MeBioS-Biosensors group, Department of BioSystems, KU Leuven, Leuven, Belgium
| | - Bernard De Baets
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium.
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Moller AG, Winston K, Ji S, Wang J, Hargita Davis MN, Solís-Lemus CR, Read TD. Genes Influencing Phage Host Range in Staphylococcus aureus on a Species-Wide Scale. mSphere 2021; 6:e01263-20. [PMID: 33441407 PMCID: PMC7845607 DOI: 10.1128/msphere.01263-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 12/16/2020] [Indexed: 12/20/2022] Open
Abstract
Staphylococcus aureus is a human pathogen that causes serious diseases, ranging from skin infections to septic shock. Bacteriophages (phages) are both natural killers of S. aureus, offering therapeutic possibilities, and important vectors of horizontal gene transfer (HGT) in the species. Here, we used high-throughput approaches to understand the genetic basis of strain-to-strain variation in sensitivity to phages, which defines the host range. We screened 259 diverse S. aureus strains covering more than 40 sequence types for sensitivity to eight phages, which were representatives of the three phage classes that infect the species. The phages were variable in host range, each infecting between 73 and 257 strains. Using genome-wide association approaches, we identified putative loci that affect host range and validated their function using USA300 transposon knockouts. In addition to rediscovering known host range determinants, we found several previously unreported genes affecting bacterial growth during phage infection, including trpA, phoR, isdB, sodM, fmtC, and relA We used the data from our host range matrix to develop predictive models that achieved between 40% and 95% accuracy. This work illustrates the complexity of the genetic basis for phage susceptibility in S. aureus but also shows that with more data, we may be able to understand much of the variation. With a knowledge of host range determination, we can rationally design phage therapy cocktails that target the broadest host range of S. aureus strains and address basic questions regarding phage-host interactions, such as the impact of phage on S. aureus evolution.IMPORTANCEStaphylococcus aureus is a widespread, hospital- and community-acquired pathogen, many strains of which are antibiotic resistant. It causes diverse diseases, ranging from local to systemic infection, and affects both the skin and many internal organs, including the heart, lungs, bones, and brain. Its ubiquity, antibiotic resistance, and disease burden make new therapies urgent. One alternative therapy to antibiotics is phage therapy, in which viruses specific to infecting bacteria clear infection. In this work, we identified and validated S. aureus genes that influence phage host range-the number of strains a phage can infect and kill-by testing strains representative of the diversity of the S. aureus species for phage host range and associating the genome sequences of strains with host range. These findings together improved our understanding of how phage therapy works in the bacterium and improve prediction of phage therapy efficacy based on the predicted host range of the infecting strain.
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Affiliation(s)
- Abraham G Moller
- Microbiology and Molecular Genetics (MMG) Program, Graduate Division of Biological and Biomedical Sciences (GDBBS), Emory University, Atlanta, Georgia, USA
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Kyle Winston
- Department of Epidemiology, Rollins School of Public Health (RSPH), Emory University, Atlanta, Georgia, USA
| | - Shiyu Ji
- Eugene Gangarosa Laboratory Research Fellowship, Emory College Online & Summer Programs, Emory College of Arts and Sciences, Atlanta, Georgia, USA
| | - Junting Wang
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Michelle N Hargita Davis
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Claudia R Solís-Lemus
- Wisconsin Institute for Discovery, Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Timothy D Read
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
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Chatterjee A, Willett JLE, Dunny GM, Duerkop BA. Phage infection and sub-lethal antibiotic exposure mediate Enterococcus faecalis type VII secretion system dependent inhibition of bystander bacteria. PLoS Genet 2021; 17:e1009204. [PMID: 33411815 PMCID: PMC7790226 DOI: 10.1371/journal.pgen.1009204] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/08/2020] [Indexed: 02/07/2023] Open
Abstract
Bacteriophages (phages) are being considered as alternative therapeutics for the treatment of multidrug resistant bacterial infections. Considering phages have narrow host-ranges, it is generally accepted that therapeutic phages will have a marginal impact on non-target bacteria. We have discovered that lytic phage infection induces transcription of type VIIb secretion system (T7SS) genes in the pathobiont Enterococcus faecalis. Membrane damage during phage infection induces T7SS gene expression resulting in cell contact dependent antagonism of different Gram positive bystander bacteria. Deletion of essB, a T7SS structural component, abrogates phage-mediated killing of bystanders. A predicted immunity gene confers protection against T7SS mediated inhibition, and disruption of its upstream LXG toxin gene rescues growth of E. faecalis and Staphylococcus aureus bystanders. Phage induction of T7SS gene expression and bystander inhibition requires IreK, a serine/threonine kinase, and OG1RF_11099, a predicted GntR-family transcription factor. Additionally, sub-lethal doses of membrane targeting and DNA damaging antibiotics activated T7SS expression independent of phage infection, triggering T7SS antibacterial activity against bystander bacteria. Our findings highlight how phage infection and antibiotic exposure of a target bacterium can affect non-target bystander bacteria and implies that therapies beyond antibiotics, such as phage therapy, could impose collateral damage to polymicrobial communities. Renewed interest in phages as alternative therapeutics to combat multi-drug resistant bacterial infections, highlights the importance of understanding the consequences of phage-bacteria interactions in the context of microbial communities. Although it is well established that phages are highly specific for their host bacterium, there is no clear consensus on whether or not phage infection (and thus phage therapy) would impose collateral damage to non-target bacteria in polymicrobial communities. Here we provide direct evidence of how phage infection of a clinically relevant pathogen triggers an intrinsic type VII secretion system (T7SS) antibacterial response that consequently restricts the growth of neighboring bacterial cells that are not susceptible to phage infection. Phage induction of T7SS activity is a stress response and in addition to phages, T7SS antagonism can be induced using sub-inhibitory concentrations of antibiotics that facilitate membrane or DNA damage. Together these data show that a bacterial pathogen responds to diverse stressors to induce T7SS activity which manifests through the antagonism of neighboring non-kin bystander bacterial cells.
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Affiliation(s)
- Anushila Chatterjee
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Julia L. E. Willett
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, United States of America
| | - Gary M. Dunny
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, United States of America
| | - Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States of America
- * E-mail:
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31
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Li J, Fokkens L, Rep M. A single gene in Fusarium oxysporum limits host range. Mol Plant Pathol 2021; 22:108-116. [PMID: 33146465 PMCID: PMC7749751 DOI: 10.1111/mpp.13011] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/24/2020] [Accepted: 09/22/2020] [Indexed: 05/07/2023]
Abstract
Fusarium oxysoporum f. sp. radicis-cucumerinum (Forc) is able to cause disease in cucumber, melon, and watermelon, while F. oxysporum f. sp. melonis (Fom) can only infect melon plants. Earlier research showed that mobile chromosomes in Forc and Fom determine the difference in host range between Forc and Fom. By closely comparing these pathogenicity chromosomes combined with RNA-sequencing data, we selected 11 candidate genes that we tested for involvement in the difference in host range between Forc and Fom. One of these candidates is a putative effector gene on the Fom pathogenicity chromosome that has nonidentical homologs on the Forc pathogenicity chromosome. Four independent Forc transformants with this gene from Fom showed strongly reduced or no pathogenicity towards cucumber, while retaining pathogenicity towards melon and watermelon. This suggests that the protein encoded by this gene is recognized by an immune receptor in cucumber plants. This is the first time that a single gene has been demonstrated to determine a difference in host specificity between formae speciales of F. oxysporum.
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Affiliation(s)
- Jiming Li
- Molecular Plant PathologyUniversity of AmsterdamAmsterdamNetherlands
| | - Like Fokkens
- Molecular Plant PathologyUniversity of AmsterdamAmsterdamNetherlands
| | - Martijn Rep
- Molecular Plant PathologyUniversity of AmsterdamAmsterdamNetherlands
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32
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Bobay LM, O’Donnell AC, Ochman H. Recombination events are concentrated in the spike protein region of Betacoronaviruses. PLoS Genet 2020; 16:e1009272. [PMID: 33332358 PMCID: PMC7775116 DOI: 10.1371/journal.pgen.1009272] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 12/31/2020] [Accepted: 11/17/2020] [Indexed: 12/24/2022] Open
Abstract
The Betacoronaviruses comprise multiple subgenera whose members have been implicated in human disease. As with SARS, MERS and now SARS-CoV-2, the origin and emergence of new variants are often attributed to events of recombination that alter host tropism or disease severity. In most cases, recombination has been detected by searches for excessively similar genomic regions in divergent strains; however, such analyses are complicated by the high mutation rates of RNA viruses, which can produce sequence similarities in distant strains by convergent mutations. By applying a genome-wide approach that examines the source of individual polymorphisms and that can be tested against null models in which recombination is absent and homoplasies can arise only by convergent mutations, we examine the extent and limits of recombination in Betacoronaviruses. We find that recombination accounts for nearly 40% of the polymorphisms circulating in populations and that gene exchange occurs almost exclusively among strains belonging to the same subgenus. Although experimental studies have shown that recombinational exchanges occur at random along the coronaviral genome, in nature, they are vastly overrepresented in regions controlling viral interaction with host cells.
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Affiliation(s)
- Louis-Marie Bobay
- Department of Biology, University of North Carolina at Greensboro, Greensboro, North Carolina, United States of America
| | - Angela C. O’Donnell
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
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Kosznik-Kwaśnicka K, Grabowski Ł, Grabski M, Kaszubski M, Górniak M, Jurczak-Kurek A, Węgrzyn G, Węgrzyn A. Bacteriophages vB_Sen-TO17 and vB_Sen-E22, Newly Isolated Viruses from Chicken Feces, Specific for Several Salmonella enterica Strains. Int J Mol Sci 2020; 21:ijms21228821. [PMID: 33233449 PMCID: PMC7700153 DOI: 10.3390/ijms21228821] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/19/2020] [Accepted: 11/19/2020] [Indexed: 11/16/2022] Open
Abstract
Two newly discovered bacteriophages, isolated from chicken feces and infecting Salmonella enterica strains, are described in this report. These phages have been named vB_Sen-TO17 and vB_Sen-E22, and we present their molecular and functional characterization. Both studied viruses are able to infect several S. enterica strains and develop lytically, but their specific host ranges differ significantly. Electron microscopic analyses of virions have been performed, and full genome sequences were determined and characterized, along with molecular phylogenetic studies. Genomes of vB_Sen-TO17 (ds DNA of 41,658 bp) and vB_Sen-E22 (dsDNA of 108,987 bp) are devoid of homologs of any known or putative gene coding for toxins or any other proteins potentially deleterious for eukaryotic cells. Both phages adsorbed efficiently (>95% adsorbed virions) within 10 min at 42 °C (resembling chicken body temperature) on cells of most tested host strains. Kinetics of lytic development of vB_Sen-TO17 and vB_Sen-E22, determined in one-step growth experiments, indicated that development is complete within 30-40 min at 42 °C, whereas burst sizes vary from 9 to 79 progeny phages per cell for vB_Sen-TO17 and from 18 to 64 for vB_Sen-E22, depending on the host strain. Virions of both phages were relatively stable (from several percent to almost 100% survivability) under various conditions, including acidic and alkaline pH values (from 3 to 12), temperatures from -80 °C to 60 °C, 70% ethanol, chloroform, and 10% DMSO. These characteristics of vB_Sen-TO17 and vB_Sen-E22 indicate that these phages might be considered in further studies on phage therapy, particularly in attempts to eliminate S. enterica from chicken intestine.
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Affiliation(s)
- Katarzyna Kosznik-Kwaśnicka
- Laboratory of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdansk, Poland; (K.K.-K.); (Ł.G.)
| | - Łukasz Grabowski
- Laboratory of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdansk, Poland; (K.K.-K.); (Ł.G.)
| | - Michał Grabski
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.G.); (M.K.); (G.W.)
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - Mateusz Kaszubski
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.G.); (M.K.); (G.W.)
| | - Marcin Górniak
- Department of Molecular Evolution, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.G.); (A.J.-K.)
| | - Agata Jurczak-Kurek
- Department of Molecular Evolution, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.G.); (A.J.-K.)
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.G.); (M.K.); (G.W.)
| | - Alicja Węgrzyn
- Laboratory of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdansk, Poland; (K.K.-K.); (Ł.G.)
- Correspondence: ; Tel.: +48-58-523-6024
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Komorizono R, Sassa Y, Horie M, Makino A, Tomonaga K. Evolutionary Selection of the Nuclear Localization Signal in the Viral Nucleoprotein Leads to Host Adaptation of the Genus Orthobornavirus. Viruses 2020; 12:v12111291. [PMID: 33187187 PMCID: PMC7698282 DOI: 10.3390/v12111291] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/23/2022] Open
Abstract
Adaptation of the viral life cycle to host cells is necessary for efficient viral infection and replication. This evolutionary process has contributed to the mechanism for determining the host range of viruses. Orthobornaviruses, members of the family Bornaviridae, are non-segmented, negative-strand RNA viruses, and several genotypes have been isolated from different vertebrate species. Previous studies revealed that some genotypes isolated from avian species can replicate in mammalian cell lines, suggesting the zoonotic potential of avian orthobornaviruses. However, the mechanism by which the host specificity of orthobornaviruses is determined has not yet been identified. In this study, we found that the infectivity of orthobornaviruses is not determined at the viral entry step, mediated by the viral glycoprotein and matrix protein. Furthermore, we demonstrated that the nuclear localization signal (NLS) sequence in the viral nucleoprotein (N) has evolved under natural selection and determines the host-specific viral polymerase activity. A chimeric mammalian orthobornavirus, which has the NLS sequence of avian orthobornavirus N, exhibited a reduced propagation efficiency in mammalian cells. Our findings indicated that nuclear transport of the viral N is a determinant of the host range of orthobornaviruses, providing insights into the evolution and host adaptation of orthobornaviruses.
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Affiliation(s)
- Ryo Komorizono
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan; (R.K.); (M.H.)
- Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto 606-8507, Japan
| | - Yukiko Sassa
- Laboratory of Veterinary Infectious Disease, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan;
| | - Masayuki Horie
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan; (R.K.); (M.H.)
- Hakubi Center for Advanced Research, Kyoto University, Kyoto 606-8507, Japan
| | - Akiko Makino
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan; (R.K.); (M.H.)
- Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto 606-8507, Japan
- Correspondence: (A.M.); (K.T.)
| | - Keizo Tomonaga
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan; (R.K.); (M.H.)
- Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto 606-8507, Japan
- Department of Molecular Virology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- Correspondence: (A.M.); (K.T.)
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Carpino C, Ferriol Safont I, Elvira‐González L, Medina V, Rubio L, Peri E, Davino S, Galipienso Torregrosa L. RNA2-encoded VP37 protein of Broad bean wilt virus 1 is a determinant of pathogenicity, host susceptibility, and a suppressor of post-transcriptional gene silencing. Mol Plant Pathol 2020; 21:1421-1435. [PMID: 32936537 PMCID: PMC7549002 DOI: 10.1111/mpp.12979] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 05/18/2020] [Revised: 07/02/2020] [Accepted: 07/02/2020] [Indexed: 06/01/2023]
Abstract
Broad bean wilt virus 1 (BBWV-1, genus Fabavirus, family Secoviridae) is a bipartite, single-stranded positive-sense RNA virus infecting many horticultural and ornamental crops worldwide. RNA1 encodes proteins involved in viral replication whereas RNA2 encodes two coat proteins (the large and small coat proteins) and two putative movement proteins (MPs) of different sizes with overlapping C-terminal regions. In this work, we determined the role played by the small putative BBWV-1 MP (VP37) on virus pathogenicity, host specificity, and suppression of post-transcriptional gene silencing (PTGS). We engineered a BBWV-1 35S-driven full-length cDNA infectious clone corresponding to BBWV-1 RNA1 and RNA2 (pBBWV1-Wt) and generated a mutant knocking out VP37 (pBBWV1-G492C). Agroinfiltration assays showed that pBBWV1-Wt, as the original BBWV-1 isolate, infected broad bean, tomato, pepper, and Nicotiana benthamiana, whereas pBBWV1-G492C did not infect pepper and tomato systemically. Also, pBBWV1-G492C induced milder symptoms in broad bean and N. benthamiana than pBBWV1-Wt. Differential retrotranscription and amplification of the (+) and (-) strands showed that pBBWV1-G492C replicated in the agroinfiltrated leaves of pepper but not in tomato. All this suggests that VP37 is a determinant of pathogenicity and host specificity. Transient expression of VP37 through a potato virus X (PVX) vector enhanced PVX symptoms and induced systemic necrosis associated with programmed cell death in N. benthamiana plants. Finally, VP37 was identified as a viral suppressor of RNA silencing by transient expression in N. benthamiana 16c plants and movement complementation of a viral construct based on turnip crinkle virus (pTCV-GFP).
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Affiliation(s)
- Caterina Carpino
- Instituto Valenciano de Investigaciones AgrariasValenciaSpain
- Department of Agricultural, Food and Forestry ScienceUniversity of PalermoPalermoItaly
| | | | - Laura Elvira‐González
- Instituto Valenciano de Investigaciones AgrariasValenciaSpain
- Departamento de BiotecnologíaEscuela Técnica Superior de Ingeniería NaturalUniversitat Politècnica de ValènciaValenciaSpain
| | - Vicente Medina
- Departamento de Producción Vegetal y Ciencia ForestalUniversitat de LleidaLleidaSpain
| | - Luis Rubio
- Instituto Valenciano de Investigaciones AgrariasValenciaSpain
| | - Ezio Peri
- Department of Agricultural, Food and Forestry ScienceUniversity of PalermoPalermoItaly
| | - Salvatore Davino
- Department of Agricultural, Food and Forestry ScienceUniversity of PalermoPalermoItaly
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Kornienko M, Kuptsov N, Gorodnichev R, Bespiatykh D, Guliaev A, Letarova M, Kulikov E, Veselovsky V, Malakhova M, Letarov A, Ilina E, Shitikov E. Contribution of Podoviridae and Myoviridae bacteriophages to the effectiveness of anti-staphylococcal therapeutic cocktails. Sci Rep 2020; 10:18612. [PMID: 33122703 PMCID: PMC7596081 DOI: 10.1038/s41598-020-75637-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/09/2020] [Indexed: 02/06/2023] Open
Abstract
Bacteriophage therapy is considered one of the most promising therapeutic approaches against multi-drug resistant bacterial infections. Infections caused by Staphylococcus aureus are very efficiently controlled with therapeutic bacteriophage cocktails, containing a number of individual phages infecting a majority of known pathogenic S. aureus strains. We assessed the contribution of individual bacteriophages comprising a therapeutic bacteriophage cocktail against S. aureus in order to optimize its composition. Two lytic bacteriophages vB_SauM-515A1 (Myoviridae) and vB_SauP-436A (Podoviridae) were isolated from the commercial therapeutic cocktail produced by Microgen (Russia). Host ranges of the phages were established on the panel of 75 S. aureus strains. Phage vB_SauM-515A1 lysed 85.3% and vB_SauP-436A lysed 68.0% of the strains, however, vB_SauP-436A was active against four strains resistant to vB_SauM-515A1, as well as to the therapeutic cocktail per se. Suboptimal results of the therapeutic cocktail application were due to extremely low vB_SauP-436A1 content in this composition. Optimization of the phage titers led to an increase in overall cocktail efficiency. Thus, one of the effective ways to optimize the phage cocktails design was demonstrated and realized by using bacteriophages of different families and lytic spectra.
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Affiliation(s)
- Maria Kornienko
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia.
| | - Nikita Kuptsov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Roman Gorodnichev
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Dmitry Bespiatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Andrei Guliaev
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Maria Letarova
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, Russia
| | - Eugene Kulikov
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, Russia
| | - Vladimir Veselovsky
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Maya Malakhova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Andrey Letarov
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, Russia
| | - Elena Ilina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Egor Shitikov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
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37
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Lauver MD, Lukacher AE. JCPyV VP1 Mutations in Progressive MultifocalLeukoencephalopathy: Altering Tropismor Mediating Immune Evasion? Viruses 2020; 12:v12101156. [PMID: 33053912 PMCID: PMC7600905 DOI: 10.3390/v12101156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 12/15/2022] Open
Abstract
Polyomaviruses are ubiquitous human pathogens that cause lifelong, asymptomatic infections in healthy individuals. Although these viruses are restrained by an intact immune system, immunocompromised individuals are at risk for developing severe diseases driven by resurgent viral replication. In particular, loss of immune control over JC polyomavirus can lead to the development of the demyelinating brain disease progressive multifocal leukoencephalopathy (PML). Viral isolates from PML patients frequently carry point mutations in the major capsid protein, VP1, which mediates virion binding to cellular glycan receptors. Because polyomaviruses are non-enveloped, VP1 is also the target of the host's neutralizing antibody response. Thus, VP1 mutations could affect tropism and/or recognition by polyomavirus-specific antibodies. How these mutations predispose susceptible individuals to PML and other JCPyV-associated CNS diseases remains to be fully elucidated. Here, we review the current understanding of polyomavirus capsid mutations and their effects on viral tropism, immune evasion, and virulence.
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38
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de Leeuw M, Baron M, Ben David O, Kushmaro A. Molecular Insights into Bacteriophage Evolution toward Its Host. Viruses 2020; 12:E1132. [PMID: 33036277 PMCID: PMC7599783 DOI: 10.3390/v12101132] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 09/24/2020] [Accepted: 09/29/2020] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages (phages), viruses that infect bacteria, are considered to be highly host-specific. To add to the knowledge about the evolution and development of bacteriophage speciation toward its host, we conducted a 21-day experiment with the broad host-range bacteriophage Aquamicrobium phage P14. We incubated the phage, which was previously isolated and enriched with the Alphaproteobacteria Aquamicrobium H14, with the Betaproteobacteria Alcaligenaceae H5. During the experiment, we observed an increase in the phage's predation efficacy towards Alcaligenaceae H5. Furthermore, genome analysis and the comparison of the bacteriophage's whole genome indicated that rather than being scattered evenly along the genome, mutations occur in specific regions. In total, 67% of the mutations with a frequency higher than 30% were located in genes that encode tail proteins, which are essential for host recognition and attachment. As control, we incubated the phage with the Alphaproteobacteria Aquamicrobium H8. In both experiments, most of the mutations appeared in the gene encoding the tail fiber protein. However, mutations in the gene encoding the tail tubular protein B were only observed when the phage was incubated with Alcaligenaceae H5. This highlights the phage's tail as a key player in its adaptation to different hosts. We conclude that mutations in the phage's genome were mainly located in tail-related regions. Further investigation is needed to fully characterize the adaptation mechanisms of the Aquamicrobium phage P14.
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Affiliation(s)
- Marina de Leeuw
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Be’er Sheva 8410501, Israel; (M.d.L.); (M.B.); (O.B.D.)
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Maayan Baron
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Be’er Sheva 8410501, Israel; (M.d.L.); (M.B.); (O.B.D.)
| | - Oshrit Ben David
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Be’er Sheva 8410501, Israel; (M.d.L.); (M.B.); (O.B.D.)
| | - Ariel Kushmaro
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Be’er Sheva 8410501, Israel; (M.d.L.); (M.B.); (O.B.D.)
- The Ilse Katz Center for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, Be’er Sheva 8410501, Israel
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39
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Nelson CW, Ardern Z, Goldberg TL, Meng C, Kuo CH, Ludwig C, Kolokotronis SO, Wei X. Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic. eLife 2020; 9:e59633. [PMID: 33001029 PMCID: PMC7655111 DOI: 10.7554/elife.59633] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/30/2020] [Indexed: 12/11/2022] Open
Abstract
Understanding the emergence of novel viruses requires an accurate and comprehensive annotation of their genomes. Overlapping genes (OLGs) are common in viruses and have been associated with pandemics but are still widely overlooked. We identify and characterize ORF3d, a novel OLG in SARS-CoV-2 that is also present in Guangxi pangolin-CoVs but not other closely related pangolin-CoVs or bat-CoVs. We then document evidence of ORF3d translation, characterize its protein sequence, and conduct an evolutionary analysis at three levels: between taxa (21 members of Severe acute respiratory syndrome-related coronavirus), between human hosts (3978 SARS-CoV-2 consensus sequences), and within human hosts (401 deeply sequenced SARS-CoV-2 samples). ORF3d has been independently identified and shown to elicit a strong antibody response in COVID-19 patients. However, it has been misclassified as the unrelated gene ORF3b, leading to confusion. Our results liken ORF3d to other accessory genes in emerging viruses and highlight the importance of OLGs.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Viral/immunology
- Antibody Specificity
- Antigens, Viral/biosynthesis
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Betacoronavirus/genetics
- Betacoronavirus/pathogenicity
- Betacoronavirus/physiology
- COVID-19
- China/epidemiology
- Chiroptera/virology
- Coronavirus/genetics
- Coronavirus Infections/epidemiology
- Coronavirus Infections/virology
- Epitopes/genetics
- Epitopes/immunology
- Europe/epidemiology
- Eutheria/virology
- Evolution, Molecular
- Gene Expression Regulation, Viral
- Genes, Overlapping
- Genes, Viral
- Genetic Variation
- Haplotypes/genetics
- Host Specificity/genetics
- Humans
- Models, Molecular
- Mutation
- Open Reading Frames/genetics
- Pandemics
- Phylogeny
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/virology
- Protein Biosynthesis
- Protein Conformation
- RNA, Viral/genetics
- SARS-CoV-2
- Sequence Alignment
- Sequence Homology, Nucleic Acid
- Viral Proteins/genetics
- Viral Proteins/immunology
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Affiliation(s)
- Chase W Nelson
- Biodiversity Research Center, Academia SinicaTaipeiTaiwan
- Institute for Comparative Genomics, American Museum of Natural HistoryNew YorkUnited States
| | - Zachary Ardern
- Chair for Microbial Ecology, Technical University of MunichFreisingGermany
| | - Tony L Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-MadisonMadisonUnited States
- Global Health Institute, University of Wisconsin-MadisonMadisonUnited States
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of MunichFreisingGermany
| | - Chen-Hao Kuo
- Biodiversity Research Center, Academia SinicaTaipeiTaiwan
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of MunichFreisingGermany
| | - Sergios-Orestis Kolokotronis
- Institute for Comparative Genomics, American Museum of Natural HistoryNew YorkUnited States
- Department of Epidemiology and Biostatistics, School of Public Health, SUNY Downstate Health Sciences UniversityBrooklynUnited States
- Institute for Genomic Health, SUNY Downstate Health Sciences UniversityBrooklynUnited States
- Division of Infectious Diseases, Department of Medicine, SUNY Downstate Health Sciences UniversityBrooklynUnited States
| | - Xinzhu Wei
- Departments of Integrative Biology and Statistics, University of California, BerkeleyBerkeleyUnited States
- Departments of Computer Science, Human Genetics, and Computational Medicine, University of California, Los AngelesLos AngelesUnited States
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40
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Wang J, Shuai L, Wang C, Liu R, He X, Zhang X, Sun Z, Shan D, Ge J, Wang X, Hua R, Zhong G, Wen Z, Bu Z. Mouse-adapted SARS-CoV-2 replicates efficiently in the upper and lower respiratory tract of BALB/c and C57BL/6J mice. Protein Cell 2020; 11:776-782. [PMID: 32749592 PMCID: PMC7401472 DOI: 10.1007/s13238-020-00767-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
MESH Headings
- Adaptation, Physiological
- Adenosine Monophosphate/administration & dosage
- Adenosine Monophosphate/analogs & derivatives
- Adenosine Monophosphate/pharmacology
- Adenosine Monophosphate/therapeutic use
- Administration, Intranasal
- Alanine/administration & dosage
- Alanine/analogs & derivatives
- Alanine/pharmacology
- Alanine/therapeutic use
- Animals
- Betacoronavirus/genetics
- Betacoronavirus/physiology
- COVID-19
- Chlorocebus aethiops
- Coronavirus Infections/drug therapy
- Coronavirus Infections/virology
- Disease Models, Animal
- Female
- Host Specificity/genetics
- Lung/pathology
- Lung/virology
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Mutation, Missense
- Nasal Mucosa/virology
- Pandemics
- Pneumonia, Viral/drug therapy
- Pneumonia, Viral/virology
- RNA, Viral/administration & dosage
- RNA, Viral/genetics
- SARS-CoV-2
- Turbinates/virology
- Vero Cells
- Viral Load
- Virus Replication
- COVID-19 Drug Treatment
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Affiliation(s)
- Jinliang Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Lei Shuai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Chong Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Renqiang Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Xijun He
- National High Containment Laboratory for Animal Diseases Control and Prevention, Harbin, 150069, China
| | - Xianfeng Zhang
- National High Containment Laboratory for Animal Diseases Control and Prevention, Harbin, 150069, China
| | - Ziruo Sun
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Dan Shan
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Jinying Ge
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Xijun Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Ronghong Hua
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Gongxun Zhong
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
| | - Zhiyuan Wen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
| | - Zhigao Bu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
- National High Containment Laboratory for Animal Diseases Control and Prevention, Harbin, 150069, China.
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41
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Sun J, Zhao W, Wang R, Zhang W, Li G, Lu M, Shao Y, Yang Y, Wang N, Gao Q, Su S. Analysis of the Codon Usage Pattern of HA and NA Genes of H7N9 Influenza A Virus. Int J Mol Sci 2020; 21:ijms21197129. [PMID: 32992529 PMCID: PMC7583936 DOI: 10.3390/ijms21197129] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 11/17/2022] Open
Abstract
Novel H7N9 influenza virus transmitted from birds to human and, since March 2013, it has caused five epidemic waves in China. Although the evolution of H7N9 viruses has been investigated, the evolutionary changes associated with codon usage are still unclear. Herein, the codon usage pattern of two surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA), was studied to understand the evolutionary changes in relation to host, epidemic wave, and pathogenicity. Both genes displayed a low codon usage bias, with HA higher than NA. The codon usage was driven by mutation pressure and natural selection, although the main contributing factor was natural selection. Additionally, the codon adaptation index (CAI) and deoptimization (RCDI) illustrated the strong adaptability of H7N9 to Gallus gallus. Similarity index (SiD) analysis showed that Homo sapiens posed a stronger selection pressure than Gallus gallus. Thus, we assume that this may be related to the gradual adaptability of the virus to human. In addition, the host strong selection pressure was validated based on CpG dinucleotide content. In conclusion, this study analyzed the usage of codons of two genes of H7N9 and expanded our understanding of H7N9 host specificity. This aids into the development of control measures against H7N9 influenza virus.
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42
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Hryckowian AJ, Merrill BD, Porter NT, Van Treuren W, Nelson EJ, Garlena RA, Russell DA, Martens EC, Sonnenburg JL. Bacteroides thetaiotaomicron-Infecting Bacteriophage Isolates Inform Sequence-Based Host Range Predictions. Cell Host Microbe 2020; 28:371-379.e5. [PMID: 32652063 PMCID: PMC8045012 DOI: 10.1016/j.chom.2020.06.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [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: 03/04/2020] [Revised: 04/22/2020] [Accepted: 06/12/2020] [Indexed: 12/21/2022]
Abstract
Our emerging view of the gut microbiome largely focuses on bacteria, while less is known about other microbial components, such as bacteriophages (phages). Though phages are abundant in the gut, very few phages have been isolated from this ecosystem. Here, we report the genomes of 27 phages from the United States and Bangladesh that infect the prevalent human gut bacterium Bacteroides thetaiotaomicron. These phages are mostly distinct from previously sequenced phages with the exception of two, which are crAss-like phages. We compare these isolates to existing human gut metagenomes, revealing similarities to previously inferred phages and additional unexplored phage diversity. Finally, we use host tropisms of these phages to identify alleles of phage structural genes associated with infectivity. This work provides a detailed view of the gut's "viral dark matter" and a framework for future efforts to further integrate isolation- and sequencing-focused efforts to understand gut-resident phages.
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Affiliation(s)
- Andrew J Hryckowian
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Bryan D Merrill
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nathan T Porter
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - William Van Treuren
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Eric J Nelson
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
| | - Rebecca A Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Eric C Martens
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Justin L Sonnenburg
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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43
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Jia N, Wang J, Shi W, Du L, Sun Y, Zhan W, Jiang JF, Wang Q, Zhang B, Ji P, Bell-Sakyi L, Cui XM, Yuan TT, Jiang BG, Yang WF, Lam TTY, Chang QC, Ding SJ, Wang XJ, Zhu JG, Ruan XD, Zhao L, Wei JT, Ye RZ, Que TC, Du CH, Zhou YH, Cheng JX, Dai PF, Guo WB, Han XH, Huang EJ, Li LF, Wei W, Gao YC, Liu JZ, Shao HZ, Wang X, Wang CC, Yang TC, Huo QB, Li W, Chen HY, Chen SE, Zhou LG, Ni XB, Tian JH, Sheng Y, Liu T, Pan YS, Xia LY, Li J, Zhao F, Cao WC. Large-Scale Comparative Analyses of Tick Genomes Elucidate Their Genetic Diversity and Vector Capacities. Cell 2020; 182:1328-1340.e13. [PMID: 32814014 DOI: 10.1016/j.cell.2020.07.023] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [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: 02/26/2020] [Revised: 06/01/2020] [Accepted: 07/17/2020] [Indexed: 12/12/2022]
Abstract
Among arthropod vectors, ticks transmit the most diverse human and animal pathogens, leading to an increasing number of new challenges worldwide. Here we sequenced and assembled high-quality genomes of six ixodid tick species and further resequenced 678 tick specimens to understand three key aspects of ticks: genetic diversity, population structure, and pathogen distribution. We explored the genetic basis common to ticks, including heme and hemoglobin digestion, iron metabolism, and reactive oxygen species, and unveiled for the first time that genetic structure and pathogen composition in different tick species are mainly shaped by ecological and geographic factors. We further identified species-specific determinants associated with different host ranges, life cycles, and distributions. The findings of this study are an invaluable resource for research and control of ticks and tick-borne diseases.
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Affiliation(s)
- Na Jia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China; Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing 100071, P.R. China
| | - Jinfeng Wang
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, P.R. China; State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Wenqiang Shi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China
| | - Lifeng Du
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, P.R. China; Institute of EcoHealth, School of Public Health, Shandong University, 44 Wenhuaxi Street, Jinan 250012, Shandong, P.R. China
| | - Yi Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China
| | - Wei Zhan
- Annoroad Gene Technology (Beijing) Company Limited, Beijing 100176, P.R. China
| | - Jia-Fu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China; Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing 100071, P.R. China
| | - Qian Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China; Institute of EcoHealth, School of Public Health, Shandong University, 44 Wenhuaxi Street, Jinan 250012, Shandong, P.R. China
| | - Bing Zhang
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Peifeng Ji
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Lesley Bell-Sakyi
- Department of Infection Biology and Microbiomes, Institute of Infection, Ecological and Veterinary Sciences, University of Liverpool, Liverpool L3 5RF, UK
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China; Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing 100071, P.R. China
| | - Ting-Ting Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China
| | - Bao-Gui Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China
| | - Wei-Fei Yang
- Annoroad Gene Technology (Beijing) Company Limited, Beijing 100176, P.R. China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Qiao-Cheng Chang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, Heilongjiang, P.R. China
| | - Shu-Jun Ding
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Communicable Disease Control and Prevention, Jinan 250014, Shandong, P.R. China
| | - Xian-Jun Wang
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Communicable Disease Control and Prevention, Jinan 250014, Shandong, P.R. China
| | - Jin-Guo Zhu
- ManZhouLi Customs District, Manzhouli 021400, Inner Mongolia, P.R. China
| | - Xiang-Dong Ruan
- Academy of Forest Inventory and Planning, State Forestry and Grassland Administration, Beijing 100714, P.R. China
| | - Lin Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China; Institute of EcoHealth, School of Public Health, Shandong University, 44 Wenhuaxi Street, Jinan 250012, Shandong, P.R. China
| | - Jia-Te Wei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China; Institute of EcoHealth, School of Public Health, Shandong University, 44 Wenhuaxi Street, Jinan 250012, Shandong, P.R. China
| | - Run-Ze Ye
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China; Institute of EcoHealth, School of Public Health, Shandong University, 44 Wenhuaxi Street, Jinan 250012, Shandong, P.R. China
| | - Teng Cheng Que
- Guangxi Zhuang Autonomous Region Terrestrial Wildlife Medical-aid and Monitoring Epidemic Diseases Research Center, Nanjing 530028, Guangxi, P.R. China
| | - Chun-Hong Du
- Yunnan Institute for Endemic Diseases Control and Prevention, Dali 671000, Yunnan, P.R. China
| | - Yu-Hao Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China
| | - Jing Xia Cheng
- Shanxi Provence Center for Disease Control and Prevention, Xian 030012, Shanxi, P.R. China
| | - Pei-Fang Dai
- Shanxi Provence Center for Disease Control and Prevention, Xian 030012, Shanxi, P.R. China
| | - Wen-Bin Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China
| | - Xiao-Hu Han
- Shenyang Agriculture University, Shenyang 110866, Liaoning, P.R. China
| | - En-Jiong Huang
- Fuzhou International Travel Healthcare Center, Fuzhou 350001, Fujian, P.R. China
| | - Lian-Feng Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China
| | - Wei Wei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China
| | - Yu-Chi Gao
- Annoroad Gene Technology (Beijing) Company Limited, Beijing 100176, P.R. China
| | - Jing-Ze Liu
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, Hebei, P.R. China
| | - Hong-Ze Shao
- Animal Husbandry and Veterinary Science Research Institute of Jilin Province, Changchun 130062, Jilin, P.R. China
| | - Xin Wang
- Qingjiangpu District Center for Disease Control and Prevention, Huai'an 223001, Jiangsu, P.R. China
| | - Chong-Cai Wang
- Hainan International Travel Healthcare Center, Haikou 570311, Hainan, P.R. China
| | - Tian-Ci Yang
- State Key Lab of Mosquito-borne Diseases, Hangzhou International Tourism Healthcare Center, Hangzhou Customs of China, Hangzhou 310012, Zhejiang, P.R. China
| | - Qiu-Bo Huo
- Mudanjiang Forestry Central Hospital, Mudanjiang 157000, Heilongjiang, P.R. China
| | - Wei Li
- Xinjiang Center for Disease Control and Prevention, Urumqi 830002, Xinjiang, P.R. China
| | - Hai-Ying Chen
- Collaboration Unit for Field Epidemiology of the State Key Laboratory for Infectious Disease Prevention and Control, Nanchang Center for Disease Control and Prevention. Nanchang 330038, Jiangxi, P.R. China
| | - Shen-En Chen
- Collaboration Unit for Field Epidemiology of the State Key Laboratory for Infectious Disease Prevention and Control, Nanchang Center for Disease Control and Prevention. Nanchang 330038, Jiangxi, P.R. China
| | - Ling-Guo Zhou
- Shaanxi Natural Reserve and Wildlife Administration Station, Xi'an 710082, Shaanxi, P.R. China
| | - Xue-Bing Ni
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Jun-Hua Tian
- Wuhan Center for Disease Control and Prevention, Wuhan 430015, Hubei, P.R. China
| | - Yue Sheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China
| | - Tao Liu
- Annoroad Gene Technology (Beijing) Company Limited, Beijing 100176, P.R. China
| | - Yu-Sheng Pan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China
| | - Luo-Yuan Xia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China
| | - Jie Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China
| | - Fangqing Zhao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, P.R. China; State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China; Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing 100071, P.R. China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, Yunan, P.R. China; Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, Zhejiang, P.R. China; University of the Chinese Academy of Sciences, Beijing 100049, P.R. China.
| | - Wu-Chun Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China; Institute of EcoHealth, School of Public Health, Shandong University, 44 Wenhuaxi Street, Jinan 250012, Shandong, P.R. China; Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing 100071, P.R. China.
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44
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Abstract
Modeling the behavior of zoonotic pandemic threats is a key component of their control. Many emerging zoonoses, such as SARS, Nipah, and Hendra, mutated from their wild type while circulating in an intermediate host population, usually a domestic species, to become more transmissible among humans, and this transmission route will only become more likely as agriculture and trade intensifies around the world. Passage through an intermediate host enables many otherwise rare diseases to become better adapted to humans, and so understanding this process with accurate mathematical models is necessary to prevent epidemics of emerging zoonoses, guide policy interventions in public health, and predict the behavior of an epidemic. In this paper, we account for a zoonotic disease mutating in an intermediate host by introducing a new mathematical model for disease transmission among three species. We present a model of these disease dynamics, including the equilibria of the system and the basic reproductive number of the pathogen, finding that in the presence of biologically realistic interspecies transmission parameters, a zoonotic disease with the capacity to mutate in an intermediate host population can establish itself in humans even if its R0 in humans is less than 1. This result and model can be used to predict the behavior of any zoonosis with an intermediate host and assist efforts to protect public health.
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Affiliation(s)
- Katherine Royce
- Dartmouth College Mathematics Department, Hanover, NH, United States of America
- * E-mail:
| | - Feng Fu
- Dartmouth College Mathematics Department, Hanover, NH, United States of America
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45
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Kennedy PG, Gagne J, Perez-Pazos E, Lofgren LA, Nguyen NH. Does fungal competitive ability explain host specificity or rarity in ectomycorrhizal symbioses? PLoS One 2020; 15:e0234099. [PMID: 32810132 PMCID: PMC7433872 DOI: 10.1371/journal.pone.0234099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 06/09/2020] [Indexed: 11/28/2022] Open
Abstract
Two common ecological assumptions are that host generalist and rare species are poorer competitors relative to host specialist and more abundant counterparts. While these assumptions have received considerable study in both plant and animals, how they apply to ectomycorrhizal fungi remains largely unknown. To investigate how interspecific competition may influence the anomalous host associations of the rare ectomycorrhizal generalist fungus, Suillus subaureus, we conducted a seedling bioassay. Pinus strobus seedlings were inoculated in single- or two-species treatments of three Suillus species: S. subaureus, S. americanus, and S. spraguei. After 4 and 8 months of growth, seedlings were harvested and scored for mycorrhizal colonization as well as dry biomass. At both time points, we found a clear competitive hierarchy among the three ectomycorrhizal fungal species: S. americanus > S. subaureus > S. spraguei, with the competitive inferior, S. spraguei, having significantly delayed colonization relative to S. americanus and S. subaureus. In the single-species treatments, we found no significant differences in the dry biomasses of P. strobus seedlings colonized by each Suillus species, suggesting none was a more effective plant symbiont. Taken together, these results indicate that the rarity and anomalous host associations exhibited by S. subaureus in natural settings are not driven by inherently poor competitive ability or host growth promotion, but that the timing of colonization is a key factor determining the outcome of ectomycorrhizal fungal competitive interactions.
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Affiliation(s)
- Peter G. Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Joe Gagne
- Department of Plant and Microbial Biology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Eduardo Perez-Pazos
- Department of Plant and Microbial Biology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Lotus A. Lofgren
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, United States of America
| | - Nhu H. Nguyen
- Department of Tropical Plant & Soil Sciences, University of Hawai’i, Manoa, Manoa, Honolulu, Hawai’i, United States of America
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46
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Furfaro LL, Payne MS, Chang BJ. Host range, morphological and genomic characterisation of bacteriophages with activity against clinical Streptococcus agalactiae isolates. PLoS One 2020; 15:e0235002. [PMID: 32574197 PMCID: PMC7310703 DOI: 10.1371/journal.pone.0235002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/06/2020] [Indexed: 01/21/2023] Open
Abstract
Streptococcus agalactiae or Group B Streptococcus (GBS) is a leading cause of sepsis in neonates. As a preventative measure prophylactic antibiotic administration is common in pregnant women colonised with GBS, but antibiotic-resistance and adverse effects on neonatal microbiomes may result. Use of bacteriophages (phages) is one option for targeted therapy. To this end, four phages (LF1 –LF4) were isolated from wastewater. They displayed lytic activity in vitro against S. agalactiae isolates collected from pregnant women and neonates, with 190/246 isolates (77.2%) and 10/10 (100%) isolates susceptible to at least one phage, respectively. Phage genomes ranged from 32,205–44,768 bp and all phages were members of the Siphoviridae family. High nucleotide identity (99.9%) was observed between LF1 and LF4, which were closely related to a putative prophage of S. agalactiae. The genome organisation of LF2 differed, and it showed similarity to a different S. agalactiae prophage, while LF3 was more closely related to a Streptococcus pyogenes phage. Lysogenic gene presence (integrase, repressor and regulatory modules), was suggestive of temperate phages. In a therapeutic context, temperate phages are not ideal candidates, however, the broad host range activity of these phages observed on clinical isolates in vitro is promising for future therapeutic approaches including bioengineered phage or lysin applications.
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Affiliation(s)
- Lucy L. Furfaro
- The School of Medicine, Division of Obstetrics and Gynaecology, The University of Western Australia, Crawley, Australia
- * E-mail:
| | - Matthew S. Payne
- The School of Medicine, Division of Obstetrics and Gynaecology, The University of Western Australia, Crawley, Australia
| | - Barbara J. Chang
- The School of Biomedical Sciences, The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Crawley, Australia
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47
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Verhagen JH, Poen M, Stallknecht DE, van der Vliet S, Lexmond P, Sreevatsan S, Poulson RL, Fouchier RAM, Lebarbenchon C. Phylogeography and Antigenic Diversity of Low-Pathogenic Avian Influenza H13 and H16 Viruses. J Virol 2020; 94:e00537-20. [PMID: 32321814 PMCID: PMC7307148 DOI: 10.1128/jvi.00537-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/13/2020] [Indexed: 11/20/2022] Open
Abstract
Low-pathogenic avian influenza viruses (LPAIVs) are genetically highly variable and have diversified into multiple evolutionary lineages that are primarily associated with wild-bird reservoirs. Antigenic variation has been described for mammalian influenza viruses and for highly pathogenic avian influenza viruses that circulate in poultry, but much less is known about antigenic variation of LPAIVs. In this study, we focused on H13 and H16 LPAIVs that circulate globally in gulls. We investigated the evolutionary history and intercontinental gene flow based on the hemagglutinin (HA) gene and used representative viruses from genetically distinct lineages to determine their antigenic properties by hemagglutination inhibition assays. For H13, at least three distinct genetic clades were evident, while for H16, at least two distinct genetic clades were evident. Twenty and ten events of intercontinental gene flow were identified for H13 and H16 viruses, respectively. At least two antigenic variants of H13 and at least one antigenic variant of H16 were identified. Amino acid positions in the HA protein that may be involved in the antigenic variation were inferred, and some of the positions were located near the receptor binding site of the HA protein, as they are in the HA protein of mammalian influenza A viruses. These findings suggest independent circulation of H13 and H16 subtypes in gull populations, as antigenic patterns do not overlap, and they contribute to the understanding of the genetic and antigenic variation of LPAIVs naturally circulating in wild birds.IMPORTANCE Wild birds play a major role in the epidemiology of low-pathogenic avian influenza viruses (LPAIVs), which are occasionally transmitted-directly or indirectly-from them to other species, including domestic animals, wild mammals, and humans, where they can cause subclinical to fatal disease. Despite a multitude of genetic studies, the antigenic variation of LPAIVs in wild birds is poorly understood. Here, we investigated the evolutionary history, intercontinental gene flow, and antigenic variation among H13 and H16 LPAIVs. The circulation of subtypes H13 and H16 seems to be maintained by a narrower host range, in particular gulls, than the majority of LPAIV subtypes and may therefore serve as a model for evolution and epidemiology of H1 to H12 LPAIVs in wild birds. The findings suggest that H13 and H16 LPAIVs circulate independently of each other and emphasize the need to investigate within-clade antigenic variation of LPAIVs in wild birds.
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Affiliation(s)
- Josanne H Verhagen
- Erasmus Medical Center, Department of Viroscience, Rotterdam, The Netherlands
- Linnaeus University, Department of Biology and Environmental Science, Kalmar, Sweden
| | - Marjolein Poen
- Erasmus Medical Center, Department of Viroscience, Rotterdam, The Netherlands
| | - David E Stallknecht
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, Department of Population Health, University of Georgia, Athens, Georgia, USA
| | | | - Pascal Lexmond
- Erasmus Medical Center, Department of Viroscience, Rotterdam, The Netherlands
| | - Srinand Sreevatsan
- Michigan State University, College of Veterinary Medicine, Department of Pathobiology and Diagnostic Investigation, East Lansing, Michigan, USA
| | - Rebecca L Poulson
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, Department of Population Health, University of Georgia, Athens, Georgia, USA
| | - Ron A M Fouchier
- Erasmus Medical Center, Department of Viroscience, Rotterdam, The Netherlands
| | - Camille Lebarbenchon
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, Department of Population Health, University of Georgia, Athens, Georgia, USA
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical, INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
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48
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Prator CA, Chooi KM, Jones D, Davy MW, MacDiarmid RM, Almeida RPP. Comparison of two different host plant genera responding to grapevine leafroll-associated virus 3 infection. Sci Rep 2020; 10:8505. [PMID: 32444786 PMCID: PMC7244584 DOI: 10.1038/s41598-020-64972-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/17/2020] [Indexed: 11/08/2022] Open
Abstract
Grapevine leafroll-associated virus 3 (GLRaV-3) is one of the most important viruses of grapevine but, despite this, there remain several gaps in our understanding of its biology. Because of its narrow host range - limited to Vitis species - and because the virus is restricted to the phloem, most GLRaV-3 research has concentrated on epidemiology and the development of detection assays. The recent discovery that GLRaV-3 can infect Nicotiana benthamiana, a plant model organism, makes new opportunities available for research in this field. We used RNA-seq to compare both V. vinifera and P1/HC-Pro N. benthamiana host responses to GLRaV-3 infection. Our analysis revealed that the majority of DEGs observed between the two hosts were unique although responses between the two hosts also showed several shared gene expression results. When comparing gene expression patterns that were shared between the two hosts, we observed the downregulation of genes associated with stress chaperones, and the induction of gene families involved in primary plant physiological processes. This is the first analysis of gene expression profiles beyond Vitis to mealybug-transmitted GLRaV-3 and demonstrates that N. benthamiana could serve as a useful tool for future studies of GLRaV-3-host interactions.
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Affiliation(s)
- Cecilia A Prator
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, 94720, USA
| | - Kar Mun Chooi
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Dan Jones
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Marcus W Davy
- The New Zealand Institute for Plant and Food Research Limited, Te Puke, New Zealand
| | - Robin M MacDiarmid
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, 94720, USA.
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49
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Wong ZS, Borrelli SLS, Coyne CC, Boyle JP. Cell type- and species-specific host responses to Toxoplasma gondii and its near relatives. Int J Parasitol 2020; 50:423-431. [PMID: 32407716 PMCID: PMC8281328 DOI: 10.1016/j.ijpara.2020.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 11/26/2019] [Revised: 03/30/2020] [Accepted: 04/03/2020] [Indexed: 10/24/2022]
Abstract
Toxoplasma gondii is remarkably unique in its ability to successfully infect vertebrate hosts from multiple phyla and can successfully infect most cells within these organisms. The infection outcome in each of these species is determined by the complex interaction between parasite and host genotype. As techniques to quantify global changes in cell function become more readily available and precise, new data are coming to light about how (i) different host cell types respond to parasitic infection and (ii) different parasite species impact the host. Here we focus on recent studies comparing the response to intracellular parasitism by different cell types and insights into understanding host-parasite interactions from comparative studies on T. gondii and its close extant relatives.
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Affiliation(s)
- Zhee S Wong
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sarah L Sokol Borrelli
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, United States
| | - Carolyn C Coyne
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Jon P Boyle
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, United States.
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50
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Li Y, Shen C, Yang L, Yang Y, Wang M, Li S, Chen F, Yang M, Peng L, Ma J, Duan Z, Li L, Liu Y. Intra-host diversity of hepatitis B virus during mother-to-child transmission: the X gene may play a key role in virus survival in children after transmission. Arch Virol 2020; 165:1279-1288. [PMID: 32240369 DOI: 10.1007/s00705-020-04597-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 02/21/2020] [Indexed: 12/23/2022]
Abstract
Mother-to-child transmission of hepatitis B virus (HBV) is the main route of transmission in Asia, and characterization of HBV quasispecies is needed to further understand virus evolution and adaptation. To understand changes in HBV during mother-to-child transmission, we enrolled nine pairs of mothers and children in the study, including a set of twins. Three groups were infected with HBV genotype C, and six groups were infected with HBV genotype B. The full-length HBV genome was amplified by PCR from serum samples before antiviral treatment, the whole viral genomes from each pair were sequenced, and the complexity and diversity of the quasispecies were analyzed. The entropy of transmitted HBV in children was found to be lower than their mothers, suggesting that there was a bottleneck effect during HBV transmission from the mother to the child. Selective evolution was shown by calculating πN and πS in the whole genomes, and the highest values were obtained for the X gene, which plays a role in viral replication and immune escape. All genotype C patients and only one genotype B pair had a πN/πS greater than 1 ratio, indicating that positive selection had occurred. In addition, quasispecies were found to be different between the twin children despite having the same mother, indicating that virus evolution is host-specific.
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Affiliation(s)
- Yanjie Li
- Department of Infectious Diseases, Shenzhen Third People's Hospital, University of South China, Shenzhen, 518112, China
| | - Chenguang Shen
- State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, No. 29, Bulan Road, Longgang District, Shenzhen, 518112, China
| | - Liuqing Yang
- State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, No. 29, Bulan Road, Longgang District, Shenzhen, 518112, China
| | - Yang Yang
- State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, No. 29, Bulan Road, Longgang District, Shenzhen, 518112, China
| | - Miao Wang
- State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, No. 29, Bulan Road, Longgang District, Shenzhen, 518112, China
| | - Shanqin Li
- State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, No. 29, Bulan Road, Longgang District, Shenzhen, 518112, China
| | - Feng Chen
- State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, No. 29, Bulan Road, Longgang District, Shenzhen, 518112, China
| | - Min Yang
- State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, No. 29, Bulan Road, Longgang District, Shenzhen, 518112, China
| | - Ling Peng
- State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, No. 29, Bulan Road, Longgang District, Shenzhen, 518112, China
| | - Jinmin Ma
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Zhongping Duan
- Difficult and complicated liver diseases and artificial liver center, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China.
| | - Liqiang Li
- BGI-Shenzhen, Shenzhen, 518083, China.
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.
| | - Yingxia Liu
- State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, No. 29, Bulan Road, Longgang District, Shenzhen, 518112, China.
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