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Cohen-Gihon I, Israeli O, Bilinsky G, Vasker B, Lazar S, Beth-Din A, Zvi A, Ghanem-Zoubi N, Atiya-Nasagi Y. Insights from genomic analysis of a novel Coxiella burnetii strain isolated in Israel. New Microbes New Infect 2024; 59:101242. [PMID: 38577384 PMCID: PMC10993178 DOI: 10.1016/j.nmni.2024.101242] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024] Open
Abstract
The diagnosis of Q fever is challenging due to nonspecific symptoms and negative standard blood culture results. Serological testing through immunofluorescence assay (IFA) is the most commonly used method for diagnosing this disease. Polymerase chain reaction (PCR) tests can also be used to detect bacterial DNA if taken at an appropriate time. Once the presence of bacteria is confirmed in a sample, an enrichment step is required before characterizing it through sequencing. Cultivating C. burnetii is challenging as it can only be isolated by inoculation into cell culture, embryonated eggs, or animals. In this article, we describe the isolation of C. burnetii from a valve specimen in Vero cells. We conducted genome sequencing and taxonomy profiling of this isolate and were able to determine its taxonomic affiliation. Furthermore, Multispacer sequence typing (MST) analysis suggests that the infection originated from a local strain of C. burnetii found around northern Israel and Lebanon. This novel strain belongs to a previously described genotype MST6, harboring the QpRS plasmid, never reported in Israel.
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Affiliation(s)
- Inbar Cohen-Gihon
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ofir Israeli
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Gal Bilinsky
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Barak Vasker
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Shirley Lazar
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Adi Beth-Din
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Anat Zvi
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | | | - Yafit Atiya-Nasagi
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
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2
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Cohen N, Simon I, Hazan O, Tal A, Tzadok H, Levin L, Girshengorn M, Mimran LC, Natan N, Baruhi T, David AB, Rosen O, Shmaya S, Borni S, Cohen N, Lupu E, Kedmi A, Zilberman O, Jayson A, Monash A, Dor E, Diamant E, Goldvaser M, Cohen-Gihon I, Israeli O, Lazar S, Shifman O, Beth-Din A, Zvi A, Oren Z, Makovitzki A, Lerer E, Mimran A, Toister E, Zichel R, Adar Y, Epstein E. Enhanced production yields of rVSV-SARS-CoV-2 vaccine using Fibra-Cel ® macrocarriers. Front Bioeng Biotechnol 2024; 12:1333548. [PMID: 38449674 PMCID: PMC10915211 DOI: 10.3389/fbioe.2024.1333548] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 02/02/2024] [Indexed: 03/08/2024] Open
Abstract
The COVID-19 pandemic has led to high global demand for vaccines to safeguard public health. To that end, our institute has developed a recombinant viral vector vaccine utilizing a modified vesicular stomatitis virus (VSV) construct, wherein the G protein of VSV is replaced with the spike protein of SARS-CoV-2 (rVSV-ΔG-spike). Previous studies have demonstrated the production of a VSV-based vaccine in Vero cells adsorbed on Cytodex 1 microcarriers or in suspension. However, the titers were limited by both the carrier surface area and shear forces. Here, we describe the development of a bioprocess for rVSV-ΔG-spike production in serum-free Vero cells using porous Fibra-Cel® macrocarriers in fixed-bed BioBLU®320 5p bioreactors, leading to high-end titers. We identified core factors that significantly improved virus production, such as the kinetics of virus production, the use of macrospargers for oxygen supply, and medium replenishment. Implementing these parameters, among others, in a series of GMP production processes improved the titer yields by at least two orders of magnitude (2e9 PFU/mL) over previously reported values. The developed process was highly effective, repeatable, and robust, creating potent and genetically stable vaccine viruses and introducing new opportunities for application in other viral vaccine platforms.
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Affiliation(s)
- Noam Cohen
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Irit Simon
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Ophir Hazan
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Arnon Tal
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Hanan Tzadok
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Lilach Levin
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Meni Girshengorn
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Lilach Cherry Mimran
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Niva Natan
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Tzadok Baruhi
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Alon Ben David
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Osnat Rosen
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Shlomo Shmaya
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Sarah Borni
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Noa Cohen
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Edith Lupu
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Adi Kedmi
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Orian Zilberman
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Avital Jayson
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Arik Monash
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Eyal Dor
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Eran Diamant
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Michael Goldvaser
- Department of Organic Chemistry, Israel Institute for Biological, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Inbar Cohen-Gihon
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Ofir Israeli
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Shirley Lazar
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Ohad Shifman
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Adi Beth-Din
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Anat Zvi
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Ziv Oren
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Arik Makovitzki
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Elad Lerer
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Avishai Mimran
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Einat Toister
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Ran Zichel
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Yaakov Adar
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Eyal Epstein
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
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3
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Yahalom-Ronen Y, Tamir H, Melamed S, Politi B, Achdout H, Erez N, Israeli O, Cohen-Gihon I, Chery Mimran L, Barlev-Gross M, Mandelboim M, Orr I, Feldmesser E, Weiss S, Beth-Din A, Paran N, Israely T. VSV-ΔG-Spike Candidate Vaccine Induces Protective Immunity and Protects K18-hACE2 Mice against SARS-CoV-2 Variants. Viruses 2023; 15:1364. [PMID: 37376662 DOI: 10.3390/v15061364] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Since the emergence of the original SARS-CoV-2, several variants were described, raising questions as to the ability of recently developed vaccine platforms to induce immunity and provide protection against these variants. Here, we utilized the K18-hACE2 mouse model to show that VSV-ΔG-spike vaccination provides protection against several SARS-CoV-2 variants: alpha, beta, gamma, and delta. We show an overall robust immune response, regardless of variant identity, leading to reduction in viral load in target organs, prevention of morbidity and mortality, as well as prevention of severe brain immune response, which follows infection with various variants. Additionally, we provide a comprehensive comparison of the brain transcriptomic profile in response to infection with different variants of SARS-CoV-2 and show how vaccination prevents these disease manifestations. Taken together, these results highlight the robust VSV-ΔG-spike protective response against diverse SARS-CoV-2 variants, as well as its promising potential against newly arising variants.
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Affiliation(s)
- Yfat Yahalom-Ronen
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Hadas Tamir
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Sharon Melamed
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Boaz Politi
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Hagit Achdout
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Noam Erez
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Ofir Israeli
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Inbar Cohen-Gihon
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Lilach Chery Mimran
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Moria Barlev-Gross
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Tel Hashomer, Ramat Gan 76100, Israel
| | - Irit Orr
- Bioinformatics Unit, Life Science Core Facilities, Weizmann Institute of Science, Rehovot 52621, Israel
| | - Ester Feldmesser
- Bioinformatics Unit, Life Science Core Facilities, Weizmann Institute of Science, Rehovot 52621, Israel
| | - Shay Weiss
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Adi Beth-Din
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Nir Paran
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Tomer Israely
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
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4
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Zaide G, Cohen-Gihon I, Shifman O, Israeli O, Aftalion M, Maoz S, Chitlaru T, Ber R, Zvi A, Steinberger-Levy I. Global transcriptomic analysis of Francisella tularensis SchuS4 differentially expressed genes in response to doxycycline or ciprofloxacin exposure. BMC Genom Data 2023; 24:23. [PMID: 37076811 PMCID: PMC10114481 DOI: 10.1186/s12863-023-01125-6] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 04/05/2023] [Indexed: 04/21/2023] Open
Abstract
OBJECTIVE As part of a research aiming at presenting an alternative approach for rapid determination of antimicrobial susceptibility by quantification of changes in expression levels of specific marker genes and gene sets, cultures of the virulent bacterial strain Francisella tularensis SchuS4 were grown in the presence of inhibitory/sub-inhibitory concentrations of either ciprofloxacin or doxycycline and their transcriptomic profiles were elucidated using differential expression analysis followed by functional annotation. DATA DESCRIPTION RNA sequencing was performed to identify differentially expressed genes (DEGs) in response to exposure of F. tularensis SchuS4 to either ciprofloxacin or doxycycline, the antibiotics of choice for Tularemia therapy. Accordingly, RNA samples were collected 2 h post antibiotic exposure and subjected to RNA sequence analysis. Transcriptomic quantification of RNA representing duplicated samples generated highly similar gene expression data. Exposure to sub-inhibitory concentration [0.5 x MIC (minimal inhibitory concentration)] of doxycycline or ciprofloxacin modulated the expression of 237 or 8 genes, respectively, while exposure to an inhibitory concentration (1 x MIC) resulted in the modulation of 583 or 234 genes, respectively. Amongst the genes modulated upon doxycycline exposure upregulation of 31 genes encoding for translation-functions could be distinguished, as well as downregulation of 14 genes encoding for functions involved in DNA transcription and repair. Ciprofloxacin exposure impacted differently the RNA sequence profile of the pathogen, resulting in upregulation of 27 genes encoding mainly DNA replication and repair functions, transmembrane transporters and molecular chaperons. In addition, 15 downregulated genes were involved in translation processes.
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Affiliation(s)
- Galia Zaide
- Israel Institute for Biological Research, Ness Ziona, Israel.
| | | | - Ohad Shifman
- Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ofir Israeli
- Israel Institute for Biological Research, Ness Ziona, Israel
| | - Moshe Aftalion
- Israel Institute for Biological Research, Ness Ziona, Israel
| | - Sharon Maoz
- Israel Institute for Biological Research, Ness Ziona, Israel
| | | | - Raphael Ber
- Israel Institute for Biological Research, Ness Ziona, Israel
| | - Anat Zvi
- Israel Institute for Biological Research, Ness Ziona, Israel
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5
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Israeli M, Finkel Y, Yahalom-Ronen Y, Paran N, Chitlaru T, Israeli O, Cohen-Gihon I, Aftalion M, Falach R, Rotem S, Elia U, Nemet I, Kliker L, Mandelboim M, Beth-Din A, Israely T, Cohen O, Stern-Ginossar N, Bercovich-Kinori A. Genome-wide CRISPR screens identify GATA6 as a proviral host factor for SARS-CoV-2 via modulation of ACE2. Nat Commun 2022; 13:2237. [PMID: 35469023 PMCID: PMC9039069 DOI: 10.1038/s41467-022-29896-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [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: 02/07/2022] [Accepted: 04/04/2022] [Indexed: 12/13/2022] Open
Abstract
The global spread of SARS-CoV-2 led to major economic and health challenges worldwide. Revealing host genes essential for infection by multiple variants of SARS-CoV-2 can provide insights into the virus pathogenesis, and facilitate the development of novel therapeutics. Here, employing a genome-scale CRISPR screen, we provide a comprehensive data-set of cellular factors that are exploited by wild type SARS-CoV-2 as well as two additional recently emerged variants of concerns (VOCs), Alpha and Beta. We identified several host factors critical for SARS-CoV-2 infection, including various components belonging to the Clathrin-dependent transport pathway, ubiquitination, Heparan sulfate biogenesis and host phosphatidylglycerol biosynthesis. Comparative analysis of the different VOCs revealed the host factors KREMEN2 and SETDB1 as potential unique candidates required only to the Alpha variant. Furthermore, the analysis identified GATA6, a zinc finger transcription factor, as an essential proviral gene for all variants inspected. We show that GATA6 directly regulates ACE2 transcription and accordingly, is critical for SARS-CoV-2 cell entry. Analysis of clinical samples collected from SARS-CoV-2 infected individuals shows elevated levels of GATA6, suggesting a role in COVID-19 pathogenesis. Finally, pharmacological inhibition of GATA6 resulted in down-modulation of ACE2 and inhibition of viral infectivity. Overall, we show GATA6 may represent a target for the development of anti-SARS-CoV-2 therapeutic strategies and reaffirm the value of the CRISPR loss-of-function screens in providing a list of potential new targets for therapeutic interventions.
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Affiliation(s)
- Ma'ayan Israeli
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Yaara Finkel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yfat Yahalom-Ronen
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Nir Paran
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Theodor Chitlaru
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ofir Israeli
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Inbar Cohen-Gihon
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Moshe Aftalion
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Reut Falach
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Shahar Rotem
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Uri Elia
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ital Nemet
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Limor Kliker
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Adi Beth-Din
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Tomer Israely
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ofer Cohen
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Bercovich-Kinori
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel.
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Guedj-Dana Y, Cohen-Gihon I, Israeli O, Shifman O, Aminov T, Rotem S, Ber R, Zvi A. Whole genome sequencing and taxonomic profiling of two Pantoea sp. isolated from environmental samples in Israel. BMC Genom Data 2022; 23:31. [PMID: 35448968 PMCID: PMC9022320 DOI: 10.1186/s12863-022-01049-7] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 04/06/2022] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE As part of a research aiming at the isolation of bacteria secreting growth inhibiting compounds, cultures of Francisella tularensis were implanted in environmental samples and monitored for inhibition zones on agar. Two antibiotic-like secreting bacteria were isolated, their genomic sequence was deciphered and taxonomic profiling analysis classified them as belonging to the Pantoea genus. DATA DESCRIPTION Two bacterial isolates exhibiting growth inhibition zones to F. tularensis (LVS) were analyzed using the Oxford Nanopore Technology (ONT). Preliminary de novo assembly of the reads was performed, followed by taxonomic profiling based on Multi Locus Sequence Analysis (MLSA) and implementation of the Average Nucleotide Identity (ANI) measure. The genomic sequences resulted in the identification of two different Pantoea species, denoted EnvD and EnvH. Subsequent de novo genome assembly generated 5 and 10 contigs for EnvD and EnvH, respectively. The largest contig (4,008,183 bps and 3,740,753 bps for EnvD and EnvH, respectively), overlaps to a major extent to the chromosome of closely related Pantoea species. ANI values calculated for both isolates revealed two apparently new species of the Pantoea genus. Our study deciphered the identity of two bacteria producing antibiotic-like compounds, and the genomic sequence revealed they represent distinct Pantoea species.
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Affiliation(s)
- Yehoudit Guedj-Dana
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Inbar Cohen-Gihon
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ofir Israeli
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ohad Shifman
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Tamar Aminov
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Shahar Rotem
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Raphael Ber
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Anat Zvi
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel.
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Mauldin MR, McCollum AM, Nakazawa YJ, Mandra A, Whitehouse ER, Davidson W, Zhao H, Gao J, Li Y, Doty J, Yinka-Ogunleye A, Akinpelu A, Aruna O, Naidoo D, Lewandowski K, Afrough B, Graham V, Aarons E, Hewson R, Vipond R, Dunning J, Chand M, Brown C, Cohen-Gihon I, Erez N, Shifman O, Israeli O, Sharon M, Schwartz E, Beth-Din A, Zvi A, Mak TM, Ng YK, Cui L, Lin RTP, Olson VA, Brooks T, Paran N, Ihekweazu C, Reynolds MG. Exportation of Monkeypox Virus From the African Continent. J Infect Dis 2022; 225:1367-1376. [PMID: 32880628 PMCID: PMC9016419 DOI: 10.1093/infdis/jiaa559] [Citation(s) in RCA: 168] [Impact Index Per Article: 84.0] [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: 06/01/2020] [Accepted: 08/28/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The largest West African monkeypox outbreak began September 2017, in Nigeria. Four individuals traveling from Nigeria to the United Kingdom (n = 2), Israel (n = 1), and Singapore (n = 1) became the first human monkeypox cases exported from Africa, and a related nosocomial transmission event in the United Kingdom became the first confirmed human-to-human monkeypox transmission event outside of Africa. METHODS Epidemiological and molecular data for exported and Nigerian cases were analyzed jointly to better understand the exportations in the temporal and geographic context of the outbreak. RESULTS Isolates from all travelers and a Bayelsa case shared a most recent common ancestor and traveled to Bayelsa, Delta, or Rivers states. Genetic variation for this cluster was lower than would be expected from a random sampling of genomes from this outbreak, but data did not support direct links between travelers. CONCLUSIONS Monophyly of exportation cases and the Bayelsa sample, along with the intermediate levels of genetic variation, suggest a small pool of related isolates is the likely source for the exported infections. This may be the result of the level of genetic variation present in monkeypox isolates circulating within the contiguous region of Bayelsa, Delta, and Rivers states, or another more restricted, yet unidentified source pool.
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Affiliation(s)
- Matthew R Mauldin
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Andrea M McCollum
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yoshinori J Nakazawa
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Anna Mandra
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Erin R Whitehouse
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Whitni Davidson
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Hui Zhao
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jinxin Gao
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yu Li
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jeffrey Doty
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | | | - Olusola Aruna
- International Health Regulations Strengthening Project, Global Public Health, Public Health England, London, United Kingdom
| | - Dhamari Naidoo
- World Health Organization Country Office, Abuja, Nigeria
| | | | | | | | - Emma Aarons
- Public Health England, London, United Kingdom
| | | | | | | | - Meera Chand
- Public Health England, London, United Kingdom
| | - Colin Brown
- Public Health England, London, United Kingdom
| | - Inbar Cohen-Gihon
- Department of Biochemistry and Molecular Biology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Noam Erez
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Ohad Shifman
- Department of Biochemistry and Molecular Biology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Ofir Israeli
- Department of Biochemistry and Molecular Biology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Melamed Sharon
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Eli Schwartz
- Institute of Tropical Medicine, Chaim Sheba Medical Center, Tel Hashomer, Israel
- Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Adi Beth-Din
- Department of Biochemistry and Molecular Biology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Anat Zvi
- Department of Biochemistry and Molecular Biology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Tze Minn Mak
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore
| | - Yi Kai Ng
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore
| | - Lin Cui
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore
| | - Raymond T P Lin
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore
| | - Victoria A Olson
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Tim Brooks
- Public Health England, London, United Kingdom
| | - Nir Paran
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel
| | | | - Mary G Reynolds
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Yahalom-Ronen Y, Erez N, Fisher M, Tamir H, Politi B, Achdout H, Melamed S, Glinert I, Weiss S, Cohen-Gihon I, Israeli O, Izak M, Mandelboim M, Caraco Y, Madar-Balakirski N, Mechaly A, Shinar E, Zichel R, Cohen D, Beth-Din A, Zvi A, Marcus H, Israely T, Paran N. Neutralization of SARS-CoV-2 Variants by rVSV-ΔG-Spike-Elicited Human Sera. Vaccines (Basel) 2022; 10:vaccines10020291. [PMID: 35214749 PMCID: PMC8879449 DOI: 10.3390/vaccines10020291] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/01/2022] [Accepted: 02/09/2022] [Indexed: 01/07/2023] Open
Abstract
The emergence of rapidly spreading variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a major challenge to the ability of vaccines and therapeutic antibodies to provide immunity. These variants contain mutations of specific amino acids that might impede vaccine efficacy. BriLife® (rVSV-ΔG-spike) is a newly developed SARS-CoV-2 vaccine candidate currently in phase II clinical trials. It is based on a replication-competent vesicular stomatitis virus (VSV) platform. The rVSV-ΔG-spike contains several spontaneously acquired spike mutations that correspond to SARS-CoV-2 variants’ mutations. We show that human sera from BriLife® vaccinees preserve comparable neutralization titers towards alpha, gamma, and delta variants and show less than a three-fold reduction in the neutralization capacity of beta and omicron compared to the original virus. Taken together, we show that human sera from BriLife® vaccinees overall maintain a neutralizing antibody response against all tested variants. We suggest that BriLife®-acquired mutations may prove advantageous against future SARS-CoV-2 VOCs.
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Affiliation(s)
- Yfat Yahalom-Ronen
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (Y.Y.-R.); (N.E.); (M.F.); (H.T.); (B.P.); (H.A.); (S.M.); (I.G.); (S.W.); (A.M.); (T.I.)
| | - Noam Erez
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (Y.Y.-R.); (N.E.); (M.F.); (H.T.); (B.P.); (H.A.); (S.M.); (I.G.); (S.W.); (A.M.); (T.I.)
| | - Morly Fisher
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (Y.Y.-R.); (N.E.); (M.F.); (H.T.); (B.P.); (H.A.); (S.M.); (I.G.); (S.W.); (A.M.); (T.I.)
| | - Hadas Tamir
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (Y.Y.-R.); (N.E.); (M.F.); (H.T.); (B.P.); (H.A.); (S.M.); (I.G.); (S.W.); (A.M.); (T.I.)
| | - Boaz Politi
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (Y.Y.-R.); (N.E.); (M.F.); (H.T.); (B.P.); (H.A.); (S.M.); (I.G.); (S.W.); (A.M.); (T.I.)
| | - Hagit Achdout
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (Y.Y.-R.); (N.E.); (M.F.); (H.T.); (B.P.); (H.A.); (S.M.); (I.G.); (S.W.); (A.M.); (T.I.)
| | - Sharon Melamed
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (Y.Y.-R.); (N.E.); (M.F.); (H.T.); (B.P.); (H.A.); (S.M.); (I.G.); (S.W.); (A.M.); (T.I.)
| | - Itai Glinert
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (Y.Y.-R.); (N.E.); (M.F.); (H.T.); (B.P.); (H.A.); (S.M.); (I.G.); (S.W.); (A.M.); (T.I.)
| | - Shay Weiss
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (Y.Y.-R.); (N.E.); (M.F.); (H.T.); (B.P.); (H.A.); (S.M.); (I.G.); (S.W.); (A.M.); (T.I.)
| | - Inbar Cohen-Gihon
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (I.C.-G.); (O.I.); (A.B.-D.); (A.Z.)
| | - Ofir Israeli
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (I.C.-G.); (O.I.); (A.B.-D.); (A.Z.)
| | - Marina Izak
- Magen David Adom, National Blood Services, Ramat Gan 52621, Israel; (M.I.); (E.S.)
| | - Michal Mandelboim
- Sheba Medical Center, Central Virology Laboratory, Ministry of Health, Tel Hashomer, Ramat Gan 52621, Israel;
| | | | - Noa Madar-Balakirski
- Department of Pharmacology, Israel Institute for Biological Research, Ness Ziona 7410001, Israel;
| | - Adva Mechaly
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (Y.Y.-R.); (N.E.); (M.F.); (H.T.); (B.P.); (H.A.); (S.M.); (I.G.); (S.W.); (A.M.); (T.I.)
| | - Eilat Shinar
- Magen David Adom, National Blood Services, Ramat Gan 52621, Israel; (M.I.); (E.S.)
| | - Ran Zichel
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (R.Z.); (H.M.)
| | - Daniel Cohen
- School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel;
| | - Adi Beth-Din
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (I.C.-G.); (O.I.); (A.B.-D.); (A.Z.)
| | - Anat Zvi
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (I.C.-G.); (O.I.); (A.B.-D.); (A.Z.)
| | - Hadar Marcus
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (R.Z.); (H.M.)
| | - Tomer Israely
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (Y.Y.-R.); (N.E.); (M.F.); (H.T.); (B.P.); (H.A.); (S.M.); (I.G.); (S.W.); (A.M.); (T.I.)
| | - Nir Paran
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (Y.Y.-R.); (N.E.); (M.F.); (H.T.); (B.P.); (H.A.); (S.M.); (I.G.); (S.W.); (A.M.); (T.I.)
- Correspondence:
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9
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Falach R, Bar-On L, Lazar S, Kadar T, Mazor O, Aftalion M, Gur D, Evgy Y, Shifman O, Aminov T, Israeli O, Cohen-Gihon I, Zaide G, Gutman H, Vagima Y, Makdasi E, Stein D, Rosenfeld R, Alcalay R, Zahavy E, Levy H, Glinert I, Ben-Shmuel A, Israely T, Melamed S, Politi B, Achdout H, Yitzhaki S, Kronman C, Sabo T. Mice with induced pulmonary morbidities display severe lung inflammation and mortality following exposure to SARS-CoV-2. JCI Insight 2021; 6:145916. [PMID: 33974566 PMCID: PMC8262502 DOI: 10.1172/jci.insight.145916] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/06/2021] [Indexed: 01/04/2023] Open
Abstract
Mice are normally unaffected by SARS coronavirus 2 (SARS-CoV-2) infection since the virus does not bind effectively to the murine version of the angiotensin-converting enzyme 2 (ACE2) receptor molecule. Here, we report that induced mild pulmonary morbidities rendered SARS-CoV-2–refractive CD-1 mice susceptible to this virus. Specifically, SARS-CoV-2 infection after application of low doses of the acute lung injury stimulants bleomycin or ricin caused severe disease in CD-1 mice, manifested by sustained body weight loss and mortality rates greater than 50%. Further studies revealed markedly higher levels of viral RNA in the lungs, heart, and serum of low-dose ricin–pretreated mice compared with non-pretreated mice. Furthermore, lung extracts prepared 2–3 days after viral infection contained subgenomic mRNA and virus particles capable of replication only when derived from the pretreated mice. The deleterious effects of SARS-CoV-2 infection were effectively alleviated by passive transfer of polyclonal or monoclonal antibodies generated against the SARS-CoV-2 receptor binding domain (RBD). Thus, viral cell entry in the sensitized mice seems to depend on viral RBD binding, albeit by a mechanism other than the canonical ACE2-mediated uptake route. This unique mode of viral entry, observed over a mildly injured tissue background, may contribute to the exacerbation of coronavirus disease 2019 (COVID-19) pathologies in patients with preexisting morbidities.
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Affiliation(s)
- Reut Falach
- Department of Biochemistry and Molecular Genetics
| | - Liat Bar-On
- Department of Biochemistry and Molecular Genetics
| | | | | | - Ohad Mazor
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel
| | | | - David Gur
- Department of Biochemistry and Molecular Genetics
| | - Yentl Evgy
- Department of Biochemistry and Molecular Genetics
| | - Ohad Shifman
- Department of Biochemistry and Molecular Genetics
| | - Tamar Aminov
- Department of Biochemistry and Molecular Genetics
| | - Ofir Israeli
- Department of Biochemistry and Molecular Genetics
| | | | - Galia Zaide
- Department of Biochemistry and Molecular Genetics
| | | | - Yaron Vagima
- Department of Biochemistry and Molecular Genetics
| | - Efi Makdasi
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Dana Stein
- Department of Biochemistry and Molecular Genetics
| | | | - Ron Alcalay
- Department of Biochemistry and Molecular Genetics
| | - Eran Zahavy
- Department of Biochemistry and Molecular Genetics
| | - Haim Levy
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Itai Glinert
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Amir Ben-Shmuel
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Tomer Israely
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Sharon Melamed
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Boaz Politi
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Hagit Achdout
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Shmuel Yitzhaki
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel
| | | | - Tamar Sabo
- Department of Biochemistry and Molecular Genetics
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10
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Zaide G, Cohen-Gihon I, Israeli O, Stein D, Shifman O, Weiss S, Simon I, Laskar O, Beth-Din A, Zvi A. Mutation Profile of SARS-CoV-2 Genome Sequences Originating from Eight Israeli Patient Isolates. Microbiol Resour Announc 2021; 10:e01387-20. [PMID: 33414330 PMCID: PMC8407753 DOI: 10.1128/mra.01387-20] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 12/17/2022] Open
Abstract
We report the genome sequences and the identification of genetic variations in eight clinical samples of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Samples were collected from nasopharyngeal swabs of symptomatic and asymptomatic individuals from five care homes for elderly and infirm persons in Israel. The sequences obtained are valuable, as they carry a newly reported nonsynonymous substitution located within the nucleoprotein open reading frame.
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Affiliation(s)
- Galia Zaide
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Inbar Cohen-Gihon
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Ofir Israeli
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Dana Stein
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Ohad Shifman
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Shay Weiss
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Irit Simon
- Department of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Orly Laskar
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Adi Beth-Din
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Anat Zvi
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
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11
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Zaide G, Elia U, Cohen-Gihon I, Israeli M, Rotem S, Israeli O, Ehrlich S, Cohen H, Lazar S, Beth-Din A, Shafferman A, Zvi A, Cohen O, Chitlaru T. Comparative Analysis of the Global Transcriptomic Response to Oxidative Stress of Bacillus anthracis htrA-Disrupted and Parental Wild Type Strains. Microorganisms 2020; 8:microorganisms8121896. [PMID: 33265965 PMCID: PMC7760947 DOI: 10.3390/microorganisms8121896] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/30/2022] Open
Abstract
We previously demonstrated that the HtrA (High Temperature Requirement A) protease/chaperone active in the quality control of protein synthesis, represents an important virulence determinant of Bacillus anthracis. Virulence attenuation of htrA-disrupted Bacillus anthracis strains was attributed to susceptibility of ΔhtrA strains to stress insults, as evidenced by affected growth under various stress conditions. Here, we report a comparative RNA-seq transcriptomic study generating a database of differentially expressed genes in the B. anthracishtrA-disrupted and wild type parental strains under oxidative stress. The study demonstrates that, apart from protease and chaperone activities, HtrA exerts a regulatory role influencing expression of more than 1000 genes under stress. Functional analysis of groups or individual genes exhibiting strain-specific modulation, evidenced (i) massive downregulation in the ΔhtrA and upregulation in the WT strains of various transcriptional regulators, (ii) downregulation of translation processes in the WT strain, and (iii) downregulation of metal ion binding functions and upregulation of sporulation-associated functions in the ΔhtrA strain. These modulated functions are extensively discussed. Fifteen genes uniquely upregulated in the wild type strain were further interrogated for their modulation in response to other stress regimens. Overexpression of one of these genes, encoding for MazG (a nucleoside triphosphate pyrophosphohydrolase involved in various stress responses in other bacteria), in the ΔhtrA strain resulted in partial alleviation of the H2O2-sensitive phenotype.
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12
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Cohen-Gihon I, Israeli O, Shifman O, Stein D, Achdout H, Weiss S, Mandelboim M, Erster O, Regev-Yochay G, Segal G, Yitzhaki S, Shapira SC, Beth-Din A, Zvi A. Coding-Complete Genome Sequences of Two SARS-CoV-2 Isolates from Early Manifestations of COVID-19 in Israel. Microbiol Resour Announc 2020; 9:e00677-20. [PMID: 32646911 PMCID: PMC7348029 DOI: 10.1128/mra.00677-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 06/19/2020] [Indexed: 11/20/2022] Open
Abstract
We announce the genome sequences of two strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolated in Israel, one imported by a traveler who returned from Japan and the second strain collected from a patient infected by a traveler returning from Italy. The sequences obtained are valuable as early manifestations for future follow-up of the local spread of the virus in Israel.
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Affiliation(s)
- Inbar Cohen-Gihon
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Ofir Israeli
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Ohad Shifman
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Dana Stein
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Hagit Achdout
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Shay Weiss
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, Ramat-Gan, Israel
| | - Oran Erster
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, Ramat-Gan, Israel
| | | | - Gad Segal
- Chaim Sheba Medical Center, Tel-Hashomer, Ramat-Gan, Israel
| | - Shmuel Yitzhaki
- Israel Institute for Biological Research, Ness-Ziona, Israel
| | | | - Adi Beth-Din
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Anat Zvi
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
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13
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Israeli O, Makdasi E, Cohen-Gihon I, Zvi A, Lazar S, Shifman O, Levy H, Gur D, Laskar O, Beth-Din A. A rapid high-throughput sequencing-based approach for the identification of unknown bacterial pathogens in whole blood. Future Sci OA 2020; 6:FSO476. [PMID: 32670604 PMCID: PMC7351085 DOI: 10.2144/fsoa-2020-0013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/09/2020] [Indexed: 01/26/2023] Open
Abstract
High-throughput DNA sequencing (HTS) of pathogens in whole blood samples is hampered by the high host/pathogen nucleic acids ratio. We describe a novel and rapid bacterial enrichment procedure whose implementation is exemplified in simulated bacteremic human blood samples. The procedure involves depletion of the host DNA, rapid HTS and bioinformatic analyses. Following this procedure, Y. pestis, F. tularensis and B. anthracis spiked-in samples displayed an improved host/pathogen DNA ratio of 2.5-5.9 orders of magnitude, in samples with bacteria spiked-in at 103-105 CFU/ml. The procedure described in this study enables rapid and detailed metagenomic profiling of pathogens within 8-9 h, circumventing the challenges imposed by the high background present in the bacteremic blood and by the unknown nature of the sample.
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Affiliation(s)
- Ofir Israeli
- Department of Biochemistry & Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Efi Makdasi
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Inbar Cohen-Gihon
- Department of Biochemistry & Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Anat Zvi
- Department of Biochemistry & Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Shirley Lazar
- Department of Biochemistry & Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ohad Shifman
- Department of Biochemistry & Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Haim Levy
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - David Gur
- Department of Biochemistry & Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Orly Laskar
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Adi Beth-Din
- Department of Biochemistry & Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
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14
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Brosh-Nissimov T, Grupel D, Abuhasira S, Leskes H, Israeli M, Lazar S, Elia U, Israeli O, Beth-Din A, Bar-Haim E, Cohen-Gihon I, Zvi A, Cohen O, Chitlaru T. Case Report: Imported Melioidosis from Goa, India to Israel, 2018. Am J Trop Med Hyg 2020; 101:580-584. [PMID: 31287043 DOI: 10.4269/ajtmh.19-0303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A previously healthy young man presented with a chronic cavitary pulmonary infection that began while in Goa, India. Burkholderia pseudomallei was cultured from sputum samples. The infection fully resolved after prolonged antibiotic treatment. Other than traveling during the monsoon season, extensive use of well-water for water-pipe smoking of cannabis was identified as a possible risk factor for infection. This is one of the first reports of travel-associated melioidosis from India. Genomic and immunological characterization suggested that the B. pseudomallei isolate collected from the reported case exhibited limited similarity to other B. pseudomallei strains.
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Affiliation(s)
- Tal Brosh-Nissimov
- Infectious Diseases Unit, Assuta Ashdod University Hospital, Ashdod, Israel.,Faculty of Health Sciences, Ben Gurion University in the Negev, Beer Sheba, Israel
| | - Daniel Grupel
- Faculty of Health Sciences, Ben Gurion University in the Negev, Beer Sheba, Israel.,Infectious Diseases Unit, Assuta Ashdod University Hospital, Ashdod, Israel
| | - Shlomi Abuhasira
- Infectious Diseases Unit, Assuta Ashdod University Hospital, Ashdod, Israel
| | - Hanna Leskes
- Microbiology Laboratory, Assuta Ashdod University Hospital, Ashdod, Israel
| | - Ma'ayan Israeli
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Shirley Lazar
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Uri Elia
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Ofir Israeli
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Adi Beth-Din
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Erez Bar-Haim
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Inbar Cohen-Gihon
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Anat Zvi
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Ofer Cohen
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Theodor Chitlaru
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
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15
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Horwitz V, Cohen-Gihon I, Egoz I, Dachir S, Cohen M, Cohen L, Gutman H, Gez R, Kadar T, Gore A, Beth-Din A, Zvi A, Zaide G, Israeli O. A comprehensive analysis of corneal mRNA levels during sulfur mustard induced ocular late pathology in the rabbit model using RNA sequencing. Exp Eye Res 2019; 184:201-212. [DOI: 10.1016/j.exer.2019.04.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 04/12/2019] [Indexed: 01/21/2023]
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16
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Israeli O, Cohen-Gihon I, Zvi A, Lazar S, Shifman O, Levy H, Tidhar A, Beth-Din A. Rapid identification of unknown pathogens in environmental samples using a high-throughput sequencing-based approach. Heliyon 2019; 5:e01793. [PMID: 31193701 PMCID: PMC6538980 DOI: 10.1016/j.heliyon.2019.e01793] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 03/31/2019] [Accepted: 05/20/2019] [Indexed: 01/06/2023] Open
Abstract
In the event of a bioterror attack, a prompt, sensitive and definite identification of the agents involved is of major concern for confirmation of the event and for mitigation of countermeasures. Whether the information from intelligence forces is limited concerning the biothreat identity or one suspects the presence of a novel or engineered agent, the genetic identification of microorganisms in an unknown sample is challenging. High-throughput sequencing (HTS) technologies can sequence a heterogeneous mixture of genetic materials with high sensitivity and speed; nevertheless, despite the enormous advantages of HTS, all previous reports have analyzed unknown samples in a timeframe of a few days to a few weeks. This timeframe might not be relevant to an emergency scenario. Here, we present an HTS-based approach for deciphering the genetic composition of unknown samples within a working day. This outcome is accomplished by a rapid library preparation procedure, short-length sequencing and a prompt bioinformatics comparison against all available microbial genomic sequences. Using this approach, as a proof of concept, we were able to detect two spiked-in biothreat agents, B. anthracis and Y. pestis, in a variety of environmental samples at relevant concentrations and within a short timeframe of eight hours.
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Affiliation(s)
- Ofir Israeli
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Inbar Cohen-Gihon
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Anat Zvi
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Shirley Lazar
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ohad Shifman
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Haim Levy
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Avital Tidhar
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Adi Beth-Din
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
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Abstract
During evolution, organisms have gained functional complexity mainly by modifying and improving existing functioning systems rather than creating new ones ab initio. Here we explore the interplay between two processes which during evolution have had major roles in the acquisition of new functions: gene duplication and protein domain rearrangements. We consider four possible evolutionary scenarios: gene families that have undergone none of these event types; only gene duplication; only domain rearrangement, or both events. We characterize each of the four evolutionary scenarios by functional attributes. Our analysis of ten fungal genomes indicates that at least for the fungi clade, species significantly appear to gain complexity by gene duplication accompanied by the expansion of existing domain architectures via rearrangements. We show that paralogs gaining new domain architectures via duplication tend to adopt new functions compared to paralogs that preserve their domain architectures. We conclude that evolution of protein families through gene duplication and domain rearrangement is correlated with their functional properties. We suggest that in general, new functions are acquired via the integration of gene duplication and domain rearrangements rather than each process acting independently.
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Affiliation(s)
- Inbar Cohen-Gihon
- Department of Human Genetics, Sackler Faculty of Medicine, Sackler Institute of Molecular Medicine, Tel Aviv University, Tel Aviv, Israel
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Cohen-Gihon I, Fong JH, Sharan R, Nussinov R, Przytycka TM, Panchenko AR. Evolution of domain promiscuity in eukaryotic genomes--a perspective from the inferred ancestral domain architectures. Mol Biosyst 2010; 7:784-92. [PMID: 21127809 DOI: 10.1039/c0mb00182a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Most eukaryotic proteins are composed of two or more domains. These assemble in a modular manner to create new proteins usually by the acquisition of one or more domains to an existing protein. Promiscuous domains which are found embedded in a variety of proteins and co-exist with many other domains are of particular interest and were shown to have roles in signaling pathways and mediating network communication. The evolution of domain promiscuity is still an open problem, mostly due to the lack of sequenced ancestral genomes. Here we use inferred domain architectures of ancestral genomes to trace the evolution of domain promiscuity in eukaryotic genomes. We find an increase in average promiscuity along many branches of the eukaryotic tree. Moreover, domain promiscuity can proceed at almost a steady rate over long evolutionary time or exhibit lineage-specific acceleration. We also observe that many signaling and regulatory domains gained domain promiscuity around the Bilateria divergence. In addition we show that those domains that played a role in the creation of two body axes and existed before the divergence of the bilaterians from fungi/metazoan achieve a boost in their promiscuities during the bilaterian evolution.
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Affiliation(s)
- Inbar Cohen-Gihon
- Sackler Institute of Molecular Medicine, Department of Human Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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Abstract
We have systematically examined the domain composition across a comprehensive set of tissue-specific, midrange and housekeeping genes as defined by their mode of expression in 52 normal mouse tissues. We show a definite correlation between the number of domains and the degree of tissue specificity. This trend is further supported by a novel analysis involving the time of origin of each domain. Genes containing metazoan-specific domains are more prevalent in signal transduction and cell-communication pathways, and are depleted in primary metabolism. Our analyses suggest that highly modular gene products have been recruited for tissue-specific functions that are required in complex organisms.
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Affiliation(s)
- Inbar Cohen-Gihon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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