101
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Wang H, Yang GX, Hu Y, Lam P, Sangha K, Siciliano D, Swenerton A, Miller R, Tilley P, Von Dadelszen P, Kalyan S, Tang P, Patel MS. Comprehensive human amniotic fluid metagenomics supports the sterile womb hypothesis. Sci Rep 2022; 12:6875. [PMID: 35477737 PMCID: PMC9046152 DOI: 10.1038/s41598-022-10869-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 04/04/2022] [Indexed: 11/17/2022] Open
Abstract
As metagenomic approaches for detecting infectious agents have improved, each tissue that was once thought to be sterile has been found to harbor a variety of microorganisms. Controversy still exists over the status of amniotic fluid, which is part of an immunologically privileged zone that is required to prevent maternal immune system rejection of the fetus. Due to this privilege, the exclusion of microbes has been proposed to be mandatory, leading to the sterile womb hypothesis. Since nucleic acid yields from amniotic fluid are very low, contaminating nucleic acid found in water, reagents and the laboratory environment frequently confound attempts to address this hypothesis. Here we present metagenomic criteria for microorganism detection and a metagenomic method able to be performed with small volumes of starting material, while controlling for exogenous contamination, to circumvent these and other pitfalls. We use this method to show that human mid-gestational amniotic fluid has no detectable virome or microbiome, supporting the sterile womb hypothesis.
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Affiliation(s)
- HanChen Wang
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Department of Physiology, McGill University, Montreal, QC, Canada
| | - Gui Xiang Yang
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Yuxiang Hu
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC, Canada.,CureImmune Therapeutics Inc., Vancouver, BC, Canada
| | - Patricia Lam
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
| | - Karan Sangha
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Dawn Siciliano
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Anne Swenerton
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Ruth Miller
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,British Columbia Centre for Disease Control, Vancouver, BC, Canada.,Contextual Genomics Inc., Vancouver, BC, Canada
| | - Peter Tilley
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,British Columbia Centre for Disease Control, Vancouver, BC, Canada
| | - Peter Von Dadelszen
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC, Canada.,Department of Women and Children's Health, School of Life Course Sciences, King's College London, London, UK
| | - Shirin Kalyan
- Division of Endocrinology and Metabolism, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Patrick Tang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,British Columbia Centre for Disease Control, Vancouver, BC, Canada.,Department of Pathology, Sidra Medical and Research Center, Doha, Qatar
| | - Millan S Patel
- BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada. .,Department of Medical Genetics, University of British Columbia, 4500 Oak St., Rm. C234, Vancouver, BC, V6H 3N1, Canada.
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102
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Simón D, Cristina J, Musto H. An overview of dinucleotide and codon usage in all viruses. Arch Virol 2022; 167:1443-1448. [PMID: 35467158 DOI: 10.1007/s00705-022-05454-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/05/2022] [Indexed: 11/30/2022]
Abstract
Viruses are, by far, the most abundant biological entities on earth. They are found in all known ecological niches and are the causative agents of many important diseases in plants and animals. From an evolutionary point of view, since viruses do not share any orthologous genes, there is a general consensus that they are polyphyletic; that is, they do not have a common ancestor. This means that they appeared several times during the course of evolution. For their life cycle, they are always obligate parasites of a free cellular life form, which can be bacteria, archaea, or eukaryotes. More complexity is added to these entities by the fact that their genetic material can be DNA or RNA (double- or single-stranded) or retrotranscribed. Given these features, we wondered if some general rules can be inferred when studying two basic genomic signatures-dinucleotides and codon usage-analyzing all available complete and non-redundant viral sequences. In spite of the obviously biased sample of sequences available, some general features appear to emerge.
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Affiliation(s)
- Diego Simón
- Laboratorio de Genómica Evolutiva, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.,Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.,Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Juan Cristina
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Héctor Musto
- Laboratorio de Genómica Evolutiva, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.
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103
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Sung I, Lee S, Pak M, Shin Y, Kim S. AutoCoV: tracking the early spread of COVID-19 in terms of the spatial and temporal patterns from embedding space by K-mer based deep learning. BMC Bioinformatics 2022; 23:149. [PMID: 35468739 PMCID: PMC9036508 DOI: 10.1186/s12859-022-04679-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 04/11/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The widely spreading coronavirus disease (COVID-19) has three major spreading properties: pathogenic mutations, spatial, and temporal propagation patterns. We know the spread of the virus geographically and temporally in terms of statistics, i.e., the number of patients. However, we are yet to understand the spread at the level of individual patients. As of March 2021, COVID-19 is wide-spread all over the world with new genetic variants. One important question is to track the early spreading patterns of COVID-19 until the virus has got spread all over the world. RESULTS In this work, we proposed AutoCoV, a deep learning method with multiple loss object, that can track the early spread of COVID-19 in terms of spatial and temporal patterns until the disease is fully spread over the world in July 2020. Performances in learning spatial or temporal patterns were measured with two clustering measures and one classification measure. For annotated SARS-CoV-2 sequences from the National Center for Biotechnology Information (NCBI), AutoCoV outperformed seven baseline methods in our experiments for learning either spatial or temporal patterns. For spatial patterns, AutoCoV had at least 1.7-fold higher clustering performances and an F1 score of 88.1%. For temporal patterns, AutoCoV had at least 1.6-fold higher clustering performances and an F1 score of 76.1%. Furthermore, AutoCoV demonstrated the robustness of the embedding space with an independent dataset, Global Initiative for Sharing All Influenza Data (GISAID). CONCLUSIONS In summary, AutoCoV learns geographic and temporal spreading patterns successfully in experiments on NCBI and GISAID datasets and is the first of its kind that learns virus spreading patterns from the genome sequences, to the best of our knowledge. We expect that this type of embedding method will be helpful in characterizing fast-evolving pandemics.
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Affiliation(s)
- Inyoung Sung
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Sangseon Lee
- Institute of Computer Technology, Seoul National University, Seoul, Republic of Korea
| | - Minwoo Pak
- Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea
| | - Yunyol Shin
- Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea
| | - Sun Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
- Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Artificial Intelligence, Seoul National University, Seoul, Republic of Korea
- AIGENDRUG Co., Ltd., Seoul, Republic of Korea
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104
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The Chronic Wound Phageome: Phage Diversity and Associations with Wounds and Healing Outcomes. Microbiol Spectr 2022; 10:e0277721. [PMID: 35435739 PMCID: PMC9248897 DOI: 10.1128/spectrum.02777-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Two leading impediments to chronic wound healing are polymicrobial infection and biofilm formation. Recent studies have characterized the bacterial fraction of these microbiomes and have begun to elucidate compositional correlations to healing outcomes. However, the factors that drive compositional shifts are still being uncovered. The virome may play an important role in shaping bacterial community structure and function. Previous work on the skin virome determined that it was dominated by bacteriophages, viruses that infect bacteria. To characterize the virome, we enrolled 20 chronic wound patients presenting at an outpatient wound care clinic in a microbiome survey, collecting swab samples from healthy skin and chronic wounds (diabetic, venous, arterial, or pressure) before and after a single, sharp debridement procedure. We investigated the virome using a virus-like particle enrichment procedure, shotgun metagenomic sequencing, and a k-mer-based, reference-dependent taxonomic classification method. Taxonomic composition, diversity, and associations with covariates are presented. We find that the wound virome is highly diverse, with many phages targeting known pathogens, and may influence bacterial community composition and functionality in ways that impact healing outcomes. IMPORTANCE Chronic wounds are an increasing medical burden. These wounds are known to be rich in microbial content, including both bacteria and bacterial viruses (phages). The viruses may play an important role in shaping bacterial community structure and function. We analyzed the virome and bacterial composition of 20 patients with chronic wounds. The viruses found in wounds are highly diverse compared to normal skin, unlike the bacterial composition, where diversity is decreased. These data represent an initial look at this relatively understudied component of the chronic wound microbiome and may help inform future phage-based interventions.
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105
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Kieft K, Anantharaman K. Virus genomics: what is being overlooked? Curr Opin Virol 2022; 53:101200. [DOI: 10.1016/j.coviro.2022.101200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/21/2021] [Accepted: 01/03/2022] [Indexed: 01/05/2023]
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106
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He WT, Hou X, Zhao J, Sun J, He H, Si W, Wang J, Jiang Z, Yan Z, Xing G, Lu M, Suchard MA, Ji X, Gong W, He B, Li J, Lemey P, Guo D, Tu C, Holmes EC, Shi M, Su S. Virome characterization of game animals in China reveals a spectrum of emerging pathogens. Cell 2022; 185:1117-1129.e8. [PMID: 35298912 PMCID: PMC9942426 DOI: 10.1016/j.cell.2022.02.014] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/10/2022] [Accepted: 02/10/2022] [Indexed: 12/27/2022]
Abstract
Game animals are wildlife species traded and consumed as food and are potential reservoirs for SARS-CoV and SARS-CoV-2. We performed a meta-transcriptomic analysis of 1,941 game animals, representing 18 species and five mammalian orders, sampled across China. From this, we identified 102 mammalian-infecting viruses, with 65 described for the first time. Twenty-one viruses were considered as potentially high risk to humans and domestic animals. Civets (Paguma larvata) carried the highest number of potentially high-risk viruses. We inferred the transmission of bat-associated coronavirus from bats to civets, as well as cross-species jumps of coronaviruses from bats to hedgehogs, from birds to porcupines, and from dogs to raccoon dogs. Of note, we identified avian Influenza A virus H9N2 in civets and Asian badgers, with the latter displaying respiratory symptoms, as well as cases of likely human-to-wildlife virus transmission. These data highlight the importance of game animals as potential drivers of disease emergence.
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Affiliation(s)
- Wan-Ting He
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China.,These authors contributed equally
| | - Xin Hou
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China.,These authors contributed equally
| | - Jin Zhao
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China.,These authors contributed equally
| | - Jiumeng Sun
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Haijian He
- Agricultural College, Jinhua Polytechnic, Jinhua 320017, China
| | - Wei Si
- MOA Key Laboratory of Animal Virology, Zhejiang University, Hangzhou 310058, China
| | - Jing Wang
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Zhiwen Jiang
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Ziqing Yan
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Gang Xing
- MOA Key Laboratory of Animal Virology, Zhejiang University, Hangzhou 310058, China
| | - Meng Lu
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Marc A. Suchard
- Department of Biostatistics, Fielding School of Public Health, and Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, the United States
| | - Xiang Ji
- Department of Mathematics, School of Science & Engineering, Tulane University, New Orleans, LA 70118, USA
| | - Wenjie Gong
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin 130062, China
| | - Biao He
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin 130062, China
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong 999077, China
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven 3000, Belgium
| | - Deyin Guo
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Changchun Tu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin 130062, China
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.,Senior authors,Correspondence: Shuo Su (); Mang Shi (); and Edward C. Holmes ()
| | - Mang Shi
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China.
| | - Shuo Su
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China.
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107
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Arizmendi Cárdenas YO, Neuenschwander S, Malaspinas AS. Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study. PeerJ 2022; 10:e12784. [PMID: 35356467 PMCID: PMC8958974 DOI: 10.7717/peerj.12784] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 12/21/2021] [Indexed: 01/10/2023] Open
Abstract
Owing to technological advances in ancient DNA, it is now possible to sequence viruses from the past to track down their origin and evolution. However, ancient DNA data is considerably more degraded and contaminated than modern data making the identification of ancient viral genomes particularly challenging. Several methods to characterise the modern microbiome (and, within this, the virome) have been developed; in particular, tools that assign sequenced reads to specific taxa in order to characterise the organisms present in a sample of interest. While these existing tools are routinely used in modern data, their performance when applied to ancient microbiome data to screen for ancient viruses remains unknown. In this work, we conducted an extensive simulation study using public viral sequences to establish which tool is the most suitable to screen ancient samples for human DNA viruses. We compared the performance of four widely used classifiers, namely Centrifuge, Kraken2, DIAMOND and MetaPhlAn2, in correctly assigning sequencing reads to the corresponding viruses. To do so, we simulated reads by adding noise typical of ancient DNA to a set of publicly available human DNA viral sequences and to the human genome. We fragmented the DNA into different lengths, added sequencing error and C to T and G to A deamination substitutions at the read termini. Then we measured the resulting sensitivity and precision for all classifiers. Across most simulations, more than 228 out of the 233 simulated viruses were recovered by Centrifuge, Kraken2 and DIAMOND, in contrast to MetaPhlAn2 which recovered only around one third. Overall, Centrifuge and Kraken2 had the best performance with the highest values of sensitivity and precision. We found that deamination damage had little impact on the performance of the classifiers, less than the sequencing error and the length of the reads. Since Centrifuge can handle short reads (in contrast to DIAMOND and Kraken2 with default settings) and since it achieve the highest sensitivity and precision at the species level across all the simulations performed, it is our recommended tool. Regardless of the tool used, our simulations indicate that, for ancient human studies, users should use strict filters to remove all reads of potential human origin. Finally, we recommend that users verify which species are present in the database used, as it might happen that default databases lack sequences for viruses of interest.
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Affiliation(s)
- Yami Ommar Arizmendi Cárdenas
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Samuel Neuenschwander
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland,Vital-IT, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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108
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Lee KA, Thomas AM, Bolte LA, Björk JR, de Ruijter LK, Armanini F, Asnicar F, Blanco-Miguez A, Board R, Calbet-Llopart N, Derosa L, Dhomen N, Brooks K, Harland M, Harries M, Leeming ER, Lorigan P, Manghi P, Marais R, Newton-Bishop J, Nezi L, Pinto F, Potrony M, Puig S, Serra-Bellver P, Shaw HM, Tamburini S, Valpione S, Vijay A, Waldron L, Zitvogel L, Zolfo M, de Vries EGE, Nathan P, Fehrmann RSN, Bataille V, Hospers GAP, Spector TD, Weersma RK, Segata N. Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma. Nat Med 2022; 28:535-544. [PMID: 35228751 PMCID: PMC8938272 DOI: 10.1038/s41591-022-01695-5] [Citation(s) in RCA: 165] [Impact Index Per Article: 82.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 01/13/2022] [Indexed: 12/13/2022]
Abstract
The composition of the gut microbiome has been associated with clinical responses to immune checkpoint inhibitor (ICI) treatment, but there is limited consensus on the specific microbiome characteristics linked to the clinical benefits of ICIs. We performed shotgun metagenomic sequencing of stool samples collected before ICI initiation from five observational cohorts recruiting ICI-naive patients with advanced cutaneous melanoma (n = 165). Integrating the dataset with 147 metagenomic samples from previously published studies, we found that the gut microbiome has a relevant, but cohort-dependent, association with the response to ICIs. A machine learning analysis confirmed the link between the microbiome and overall response rates (ORRs) and progression-free survival (PFS) with ICIs but also revealed limited reproducibility of microbiome-based signatures across cohorts. Accordingly, a panel of species, including Bifidobacterium pseudocatenulatum, Roseburia spp. and Akkermansia muciniphila, associated with responders was identified, but no single species could be regarded as a fully consistent biomarker across studies. Overall, the role of the human gut microbiome in ICI response appears more complex than previously thought, extending beyond differing microbial species simply present or absent in responders and nonresponders. Future studies should adopt larger sample sizes and take into account the complex interplay of clinical factors with the gut microbiome over the treatment course.
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Affiliation(s)
- Karla A Lee
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | - Laura A Bolte
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Johannes R Björk
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Laura Kist de Ruijter
- Department of Medical Oncology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | | | | | | | - Ruth Board
- Department of Oncology, Lancashire Teaching Hospitals NHS Trust, Preston, UK
| | - Neus Calbet-Llopart
- Dermatology Department, Hospital Clínic Barcelona, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras, Instituto de Salud Carlos III, Barcelona, Spain
| | - Lisa Derosa
- U1015 INSERM, University Paris Saclay, Gustave Roussy Cancer Center and Oncobiome Network, Villejuif-Grand-Paris, France
| | - Nathalie Dhomen
- Molecular Oncology Group, CRUK Manchester Institute, University of Manchester, Manchester, UK
| | - Kelly Brooks
- Molecular Oncology Group, CRUK Manchester Institute, University of Manchester, Manchester, UK
| | - Mark Harland
- Division of Haematology and Immunology, Institute of Medical Research at St. James's, University of Leeds, Leeds, UK
| | - Mark Harries
- Biochemical and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS and University of Barcelona, Barcelona, Spain
- Department of Medical Oncology, Guys Cancer Centre, Guys and St Thomas's NHS Trust, London, UK
| | - Emily R Leeming
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Paul Lorigan
- The Christie NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Richard Marais
- Molecular Oncology Group, CRUK Manchester Institute, University of Manchester, Manchester, UK
| | - Julia Newton-Bishop
- Division of Haematology and Immunology, Institute of Medical Research at St. James's, University of Leeds, Leeds, UK
| | - Luigi Nezi
- European Institute of Oncology (Istituto Europeo di Oncologia, IRCSS), Milan, Italy
| | | | - Miriam Potrony
- Centro de Investigación Biomédica en Red en Enfermedades Raras, Instituto de Salud Carlos III, Barcelona, Spain
- Biochemical and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS and University of Barcelona, Barcelona, Spain
| | - Susana Puig
- Centro de Investigación Biomédica en Red en Enfermedades Raras, Instituto de Salud Carlos III, Barcelona, Spain
- Biochemical and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS and University of Barcelona, Barcelona, Spain
| | | | - Heather M Shaw
- Department of Medical Oncology, Mount Vernon Cancer Centre, Northwood, UK
| | - Sabrina Tamburini
- European Institute of Oncology (Istituto Europeo di Oncologia, IRCSS), Milan, Italy
| | - Sara Valpione
- Molecular Oncology Group, CRUK Manchester Institute, University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester, UK
| | - Amrita Vijay
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Rheumatology & Orthopaedics Division, School of Medicine, University of Nottingham, Nottingham, UK
| | - Levi Waldron
- Department CIBIO, University of Trento, Trento, Italy
- Graduate School of Public Health and Health Policy, City University of New York, New York, NY, USA
| | - Laurence Zitvogel
- U1015 INSERM, University Paris Saclay, Gustave Roussy Cancer Center and Oncobiome Network, Villejuif-Grand-Paris, France
| | - Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | - Elisabeth G E de Vries
- Department of Medical Oncology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Paul Nathan
- Biochemical and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS and University of Barcelona, Barcelona, Spain
| | - Rudolf S N Fehrmann
- Department of Medical Oncology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Véronique Bataille
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Dermatology, Mount Vernon Cancer Centre, Northwood, UK
| | - Geke A P Hospers
- Department of Medical Oncology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands.
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
- European Institute of Oncology (Istituto Europeo di Oncologia, IRCSS), Milan, Italy.
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109
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Muñoz-Baena L, Poon AFY. Using networks to analyze and visualize the distribution of overlapping genes in virus genomes. PLoS Pathog 2022; 18:e1010331. [PMID: 35202429 PMCID: PMC8903798 DOI: 10.1371/journal.ppat.1010331] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 03/08/2022] [Accepted: 02/02/2022] [Indexed: 11/19/2022] Open
Abstract
Gene overlap occurs when two or more genes are encoded by the same nucleotides. This phenomenon is found in all taxonomic domains, but is particularly common in viruses, where it may increase the information content of compact genomes or influence the creation of new genes. Here we report a global comparative study of overlapping open reading frames (OvRFs) of 12,609 virus reference genomes in the NCBI database. We retrieved metadata associated with all annotated open reading frames (ORFs) in each genome record to calculate the number, length, and frameshift of OvRFs. Our results show that while the number of OvRFs increases with genome length, they tend to be shorter in longer genomes. The majority of overlaps involve +2 frameshifts, predominantly found in dsDNA viruses. Antisense overlaps in which one of the ORFs was encoded in the same frame on the opposite strand (−0) tend to be longer. Next, we develop a new graph-based representation of the distribution of overlaps among the ORFs of genomes in a given virus family. In the absence of an unambiguous partition of ORFs by homology at this taxonomic level, we used an alignment-free k-mer based approach to cluster protein coding sequences by similarity. We connect these clusters with two types of directed edges to indicate (1) that constituent ORFs are adjacent in one or more genomes, and (2) that these ORFs overlap. These adjacency graphs not only provide a natural visualization scheme, but also a novel statistical framework for analyzing the effects of gene- and genome-level attributes on the frequencies of overlaps.
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Affiliation(s)
- Laura Muñoz-Baena
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Art F. Y. Poon
- Department of Microbiology and Immunology, Western University, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
- * E-mail:
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GIRALDO RAMÍREZ SUSANA, SIERRA MEJÍA ANDREA, OSPINA ORTIZ MARIAISABELLA, HIGUITA VALENCIA MÓNICA, GALLO GARCÍA YULIANA, GUTIÉRREZ SÁNCHEZ PABLOANDRÉS, Marín Montoya MA. DETECCIÓN Y CARACTERIZACIÓN MOLECULAR DEL POTATO VIRUS B (PVB) EN CULTIVOS DE PAPA CRIOLLA (Solanum phureja) EN ANTIOQUIA. ACTA BIOLÓGICA COLOMBIANA 2022. [DOI: 10.15446/abc.v27n2.89422] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
La papa criolla (Solanum phureja Juz. & Bukasov) es uno de los principales productos agrícolas de la región Andina de Colombia. Su siembra ocurre principalmente en pequeñas parcelas con deficiencias técnicas y bajos rendimientos. Las enfermedades de origen viral son una de las principales limitantes de este cultivo, siendo los virus PYVV, PVS, PLRV y PVV algunos de los más importantes. El nivel de conocimiento que se tiene del viroma de la papa criolla en Colombia es incipiente. En este estudio utilizando técnicas moleculares como secuenciación de alto rendimiento (HTS) y RT-PCR en tiempo real (RT-qPCR), a partir de muestras de tejido foliar de plantas procedentes de diferentes lotes de papa criolla en Antioquia (Colombia), se detectó por primera vez para el país la infección del Potato virus B (PVB), un nepovirus hasta ahora sólo registrado en Perú. Mediante análisis bioinformáticos fue posible el ensamblaje de la mayor parte del genoma de PVB, consistente de dos segmentos de 7.126 nt (ARN1) y 4.298 nt (ARN2) que codifican para dos poliproteínas (P1 y P2). Con las secuencias obtenidas se diseñaron primers específicos para la detección del PVB por RT-qPCR y RT-PCR convencional. Los resultados indicaron niveles medios de prevalencia (35%) del PVB en los cultivos de papa criolla evaluados y su ausencia en las 20 muestras evaluadas de S. tuberosum var. Diacol-Capiro. Con las técnicas aquí empleadas, se sugiere el establecimiento de un programa de seguimiento epidemiológico de PVB en Colombia y otros países andinos.
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111
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Wang X, Sacramento CQ, Jockusch S, Chaves OA, Tao C, Fintelman-Rodrigues N, Chien M, Temerozo JR, Li X, Kumar S, Xie W, Patel DJ, Meyer C, Garzia A, Tuschl T, Bozza PT, Russo JJ, Souza TML, Ju J. Combination of antiviral drugs inhibits SARS-CoV-2 polymerase and exonuclease and demonstrates COVID-19 therapeutic potential in viral cell culture. Commun Biol 2022; 5:154. [PMID: 35194144 PMCID: PMC8863796 DOI: 10.1038/s42003-022-03101-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 02/02/2022] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 has an exonuclease-based proofreader, which removes nucleotide inhibitors such as Remdesivir that are incorporated into the viral RNA during replication, reducing the efficacy of these drugs for treating COVID-19. Combinations of inhibitors of both the viral RNA-dependent RNA polymerase and the exonuclease could overcome this deficiency. Here we report the identification of hepatitis C virus NS5A inhibitors Pibrentasvir and Ombitasvir as SARS-CoV-2 exonuclease inhibitors. In the presence of Pibrentasvir, RNAs terminated with the active forms of the prodrugs Sofosbuvir, Remdesivir, Favipiravir, Molnupiravir and AT-527 were largely protected from excision by the exonuclease, while in the absence of Pibrentasvir, there was rapid excision. Due to its unique structure, Tenofovir-terminated RNA was highly resistant to exonuclease excision even in the absence of Pibrentasvir. Viral cell culture studies also demonstrate significant synergy using this combination strategy. This study supports the use of combination drugs that inhibit both the SARS-CoV-2 polymerase and exonuclease for effective COVID-19 treatment.
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Grants
- P30 CA008748 NCI NIH HHS
- This work was supported by the Jack Ma Foundation, a gift from Columbia Engineering Member of the Board of Visitors Dr. Bing Zhao, and Fast Grants (to Jingyue Ju), the Maloris Foundation and the Memorial Sloan-Kettering Core Grant (P30CA008748) (to Dinshaw J. Patel), a grant from The JPB Foundation to Rockefeller University (to Thomas Tuschl). Funding was also provided by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, 441019/2020-0, 307162/2017-6), Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ, E-26/210.182/2020, E-26/201.067/2021, E-26/210.112/2020) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) - Finance Code 001 (to Thiago Moreno L. Souza and Patricia T. Bozza). CNPq, CAPES and FAPERJ also support the National Institutes of Science and Technology Program (INCT-IDPN, 465313/2014-0). Oswaldo Cruz Foundation/FIOCRUZ supports this study under the auspices of the Inova Program (B3-Bovespa funding, VGPDI-032-ARVC-20) (to Thiago Moreno L. Souza). Dr. Andre Sampaio from Farmanguinhos, platform RPT11M, is acknowledged for kindly donating the Calu-3 cells. We thank Dr. Andrew Owen from the University of Liverpool for insightful discussions.
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Affiliation(s)
- Xuanting Wang
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Carolina Q Sacramento
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology for Innovation on Diseases of Neglected Population (INCT/IDPN), Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Steffen Jockusch
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Otávio Augusto Chaves
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology for Innovation on Diseases of Neglected Population (INCT/IDPN), Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Chuanjuan Tao
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Natalia Fintelman-Rodrigues
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology for Innovation on Diseases of Neglected Population (INCT/IDPN), Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Minchen Chien
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Jairo R Temerozo
- Laboratory on Thymus Research, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology on Neuroimmunomodulation (INCT/NIM), Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Xiaoxu Li
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Shiv Kumar
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Wei Xie
- Laboratory of Structural Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Dinshaw J Patel
- Laboratory of Structural Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Cindy Meyer
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY, 10065, USA
| | - Aitor Garzia
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY, 10065, USA
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY, 10065, USA
| | - Patrícia T Bozza
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - James J Russo
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Thiago Moreno L Souza
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil.
- National Institute for Science and Technology for Innovation on Diseases of Neglected Population (INCT/IDPN), Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil.
| | - Jingyue Ju
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA.
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA.
- Department of Molecular Pharmacology and Therapeutics, Columbia University, New York, NY, 10032, USA.
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Wu F, Speth DR, Philosof A, Crémière A, Narayanan A, Barco RA, Connon SA, Amend JP, Antoshechkin IA, Orphan VJ. Unique mobile elements and scalable gene flow at the prokaryote-eukaryote boundary revealed by circularized Asgard archaea genomes. Nat Microbiol 2022; 7:200-212. [PMID: 35027677 PMCID: PMC8813620 DOI: 10.1038/s41564-021-01039-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/29/2021] [Indexed: 12/22/2022]
Abstract
Eukaryotic genomes are known to have garnered innovations from both archaeal and bacterial domains but the sequence of events that led to the complex gene repertoire of eukaryotes is largely unresolved. Here, through the enrichment of hydrothermal vent microorganisms, we recovered two circularized genomes of Heimdallarchaeum species that belong to an Asgard archaea clade phylogenetically closest to eukaryotes. These genomes reveal diverse mobile elements, including an integrative viral genome that bidirectionally replicates in a circular form and aloposons, transposons that encode the 5,000 amino acid-sized proteins Otus and Ephialtes. Heimdallaechaeal mobile elements have garnered various genes from bacteria and bacteriophages, likely playing a role in shuffling functions across domains. The number of archaea- and bacteria-related genes follow strikingly different scaling laws in Asgard archaea, exhibiting a genome size-dependent ratio and a functional division resembling the bacteria- and archaea-derived gene repertoire across eukaryotes. Bacterial gene import has thus likely been a continuous process unaltered by eukaryogenesis and scaled up through genome expansion. Our data further highlight the importance of viewing eukaryogenesis in a pan-Asgard context, which led to the proposal of a conceptual framework, that is, the Heimdall nucleation-decentralized innovation-hierarchical import model that accounts for the emergence of eukaryotic complexity.
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Affiliation(s)
- Fabai Wu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Daan R Speth
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Alon Philosof
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Antoine Crémière
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Aditi Narayanan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Roman A Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Stephanie A Connon
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Jan P Amend
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Igor A Antoshechkin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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113
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Bovo S, Schiavo G, Bolner M, Ballan M, Fontanesi L. Mining livestock genome datasets for an unconventional characterization of animal DNA viromes. Genomics 2022; 114:110312. [DOI: 10.1016/j.ygeno.2022.110312] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 01/16/2022] [Accepted: 02/06/2022] [Indexed: 11/04/2022]
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114
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Rout RK, Hassan SS, Sheikh S, Umer S, Sahoo KS, Gandomi AH. Feature-extraction and analysis based on spatial distribution of amino acids for SARS-CoV-2 Protein sequences. Comput Biol Med 2022; 141:105024. [PMID: 34815067 PMCID: PMC8577876 DOI: 10.1016/j.compbiomed.2021.105024] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/15/2021] [Accepted: 11/04/2021] [Indexed: 12/28/2022]
Abstract
BACKGROUND AND OBJECTIVE The world is currently facing a global emergency due to COVID-19, which requires immediate strategies to strengthen healthcare facilities and prevent further deaths. To achieve effective remedies and solutions, research on different aspects, including the genomic and proteomic level characterizations of SARS-CoV-2, are critical. In this work, the spatial representation/composition and distribution frequency of 20 amino acids across the primary protein sequences of SARS-CoV-2 were examined according to different parameters. METHOD To identify the spatial distribution of amino acids over the primary protein sequences of SARS-CoV-2, the Hurst exponent and Shannon entropy were applied as parameters to fetch the autocorrelation and amount of information over the spatial representations. The frequency distribution of each amino acid over the protein sequences was also evaluated. In the case of a one-dimensional sequence, the Hurst exponent (HE) was utilized due to its linear relationship with the fractal dimension (D), i.e. D+HE=2, to characterize fractality. Moreover, binary Shannon entropy was considered to measure the uncertainty in a binary sequence then further applied to calculate amino acid conservation in the primary protein sequences. RESULTS AND CONCLUSION Fourteen (14) SARS-CoV protein sequences were evaluated and compared with 105 SARS-CoV-2 proteins. The simulation results demonstrate the differences in the collected information about the amino acid spatial distribution in the SARS-CoV-2 and SARS-CoV proteins, enabling researchers to distinguish between the two types of CoV. The spatial arrangement of amino acids also reveals similarities and dissimilarities among the important structural proteins, E, M, N and S, which is pivotal to establish an evolutionary tree with other CoV strains.
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Affiliation(s)
- Ranjeet Kumar Rout
- Department of Computer Science & Engineering, National Institute of Technology Srinagar, Hazratbal, Jammu and Kashmir, India.
| | - Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, 721140, India.
| | - Sabha Sheikh
- Department of Computer Science & Engineering, National Institute of Technology Srinagar, Hazratbal, Jammu and Kashmir, India.
| | - Saiyed Umer
- Department of Computer Science and Engineering, Aliah University, Kolkata, India.
| | - Kshira Sagar Sahoo
- Department of Computer Science and Engineering, SRM University, Amaravati, AP, 522240, India.
| | - Amir H Gandomi
- Faculty of Engineering and Information Technology, University of Technology Sydney, NSW, Australia.
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115
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Guzzo GL, Andrews JM, Weyrich LS. The Neglected Gut Microbiome: Fungi, Protozoa, and Bacteriophages in Inflammatory Bowel Disease. Inflamm Bowel Dis 2022; 28:1112-1122. [PMID: 35092426 PMCID: PMC9247841 DOI: 10.1093/ibd/izab343] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Indexed: 12/14/2022]
Abstract
The gut microbiome has been implicated in the pathogenesis of inflammatory bowel disease (IBD). Studies suggest that the IBD gut microbiome is less diverse than that of the unaffected population, a phenomenon often referred to as dysbiosis. However, these studies have heavily focused on bacteria, while other intestinal microorganisms-fungi, protozoa, and bacteriophages-have been neglected. Of the nonbacterial microbes that have been studied in relation to IBD, most are thought to be pathogens, although there is evidence that some of these species may instead be harmless commensals. In this review, we discuss the nonbacterial gut microbiome of IBD, highlighting the current biases, limitations, and outstanding questions that can be addressed with high-throughput DNA sequencing methods. Further, we highlight the importance of studying nonbacterial microorganisms alongside bacteria for a comprehensive view of the whole IBD biome and to provide a more precise definition of dysbiosis in patients. With the rise in popularity of microbiome-altering therapies for the treatment of IBD, such as fecal microbiota transplantation, it is important that we address these knowledge gaps to ensure safe and effective treatment of patients.
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Affiliation(s)
- Gina L Guzzo
- Address correspondence to: Gina L. Guzzo, The University of Adelaide, Adelaide, South Australia, Australia ()
| | - Jane M Andrews
- Inflammatory Bowel Disease Service, Department of Gastroenterology and Hepatology, Royal Adelaide Hospital and School of Medicine, Faculty of Health Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Laura S Weyrich
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia,Department of Anthropology and Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA, USA
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116
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Forero-Junco LM, Alanin KWS, Djurhuus AM, Kot W, Gobbi A, Hansen LH. Bacteriophages Roam the Wheat Phyllosphere. Viruses 2022; 14:v14020244. [PMID: 35215838 PMCID: PMC8876510 DOI: 10.3390/v14020244] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 12/13/2022] Open
Abstract
The phyllosphere microbiome plays an important role in plant fitness. Recently, bacteriophages have been shown to play a role in shaping the bacterial community composition of the phyllosphere. However, no studies on the diversity and abundance of phyllosphere bacteriophage communities have been carried out until now. In this study, we extracted, sequenced, and characterized the dsDNA and ssDNA viral community from a phyllosphere for the first time. We sampled leaves from winter wheat (Triticum aestivum), where we identified a total of 876 virus operational taxonomic units (vOTUs), mostly predicted to be bacteriophages with a lytic lifestyle. Remarkably, 848 of these vOTUs corresponded to new viral species, and we estimated a minimum of 2.0 × 106 viral particles per leaf. These results suggest that the wheat phyllosphere harbors a large and active community of novel bacterial viruses. Phylloviruses have potential applications as biocontrol agents against phytopathogenic bacteria or as microbiome modulators to increase plant growth-promoting bacteria.
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Affiliation(s)
- Laura Milena Forero-Junco
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (K.W.S.A.); (A.M.D.); (W.K.); (A.G.)
- Correspondence: (L.M.F.-J.); (L.H.H.)
| | - Katrine Wacenius Skov Alanin
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (K.W.S.A.); (A.M.D.); (W.K.); (A.G.)
- Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark
| | - Amaru Miranda Djurhuus
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (K.W.S.A.); (A.M.D.); (W.K.); (A.G.)
| | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (K.W.S.A.); (A.M.D.); (W.K.); (A.G.)
| | - Alex Gobbi
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (K.W.S.A.); (A.M.D.); (W.K.); (A.G.)
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (K.W.S.A.); (A.M.D.); (W.K.); (A.G.)
- Correspondence: (L.M.F.-J.); (L.H.H.)
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117
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Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes. Proc Natl Acad Sci U S A 2022; 119:2113118119. [PMID: 35022216 PMCID: PMC8795541 DOI: 10.1073/pnas.2113118119] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2021] [Indexed: 12/21/2022] Open
Abstract
During the COVID pandemic, new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants emerge and spread, some being of major concern due to their increased infectivity or capacity to reduce vaccine efficiency. Anticipating mutations, which might give rise to new variants, would be of great interest. We construct sequence models predicting how mutable SARS-CoV-2 positions are, using a single SARS-CoV-2 sequence and databases of other coronaviruses. Predictions are tested against available mutagenesis data and the observed variability of SARS-CoV-2 proteins. Interestingly, predictions agree increasingly with observations, as more SARS-CoV-2 sequences become available. Combining predictions with immunological data, we find an overrepresentation of mutations in current variants of concern. The approach may become relevant for potential outbreaks of future viral diseases. The emergence of new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major concern given their potential impact on the transmissibility and pathogenicity of the virus as well as the efficacy of therapeutic interventions. Here, we predict the mutability of all positions in SARS-CoV-2 protein domains to forecast the appearance of unseen variants. Using sequence data from other coronaviruses, preexisting to SARS-CoV-2, we build statistical models that not only capture amino acid conservation but also more complex patterns resulting from epistasis. We show that these models are notably superior to conservation profiles in estimating the already observable SARS-CoV-2 variability. In the receptor binding domain of the spike protein, we observe that the predicted mutability correlates well with experimental measures of protein stability and that both are reliable mutability predictors (receiver operating characteristic areas under the curve ∼0.8). Most interestingly, we observe an increasing agreement between our model and the observed variability as more data become available over time, proving the anticipatory capacity of our model. When combined with data concerning the immune response, our approach identifies positions where current variants of concern are highly overrepresented. These results could assist studies on viral evolution and future viral outbreaks and, in particular, guide the exploration and anticipation of potentially harmful future SARS-CoV-2 variants.
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118
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Gulyaeva A, Garmaeva S, Ruigrok RAAA, Wang D, Riksen NP, Netea MG, Wijmenga C, Weersma RK, Fu J, Vila AV, Kurilshikov A, Zhernakova A. Discovery, diversity, and functional associations of crAss-like phages in human gut metagenomes from four Dutch cohorts. Cell Rep 2022; 38:110204. [PMID: 35021085 DOI: 10.1016/j.celrep.2021.110204] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/03/2021] [Accepted: 12/13/2021] [Indexed: 12/16/2022] Open
Abstract
The crAss-like phages are a diverse group of related viruses that includes some of the most abundant viruses of the human gut. To explore their diversity and functional role in human population and clinical cohorts, we analyze gut metagenomic data collected from 1,950 individuals from the Netherlands. We identify 1,556 crAss-like phage genomes, including 125 species-level and 32 genus-level clusters absent from the reference databases used. Analysis of their genomic features shows that closely related crAss-like phages can possess strikingly divergent regions responsible for transcription, presumably acquired through recombination. Prediction of crAss-like phage hosts points primarily to bacteria of the phylum Bacteroidetes, consistent with previous reports. Finally, we explore the temporal stability of crAss-like phages over a 4-year period and identify associations between the abundance of crAss-like phages and several human phenotypes, including depletion of crAss-like phages in inflammatory bowel disease patients.
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Affiliation(s)
- Anastasia Gulyaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands.
| | - Sanzhima Garmaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Renate A A A Ruigrok
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands; Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Daoming Wang
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Niels P Riksen
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen 6525GA, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen 6525GA, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Rinse K Weersma
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands; Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands; Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands.
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119
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Conserved Motifs and Domains in Members of Pospiviroidae. Cells 2022; 11:cells11020230. [PMID: 35053346 PMCID: PMC8774013 DOI: 10.3390/cells11020230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/28/2021] [Accepted: 01/07/2022] [Indexed: 12/18/2022] Open
Abstract
In 1985, Keese and Symons proposed a hypothesis on the sequence and secondary structure of viroids from the family Pospiviroidae: their secondary structure can be subdivided into five structural and functional domains and “viroids have evolved by rearrangement of domains between different viroids infecting the same cell and subsequent mutations within each domain”; this article is one of the most cited in the field of viroids. Employing the pairwise alignment method used by Keese and Symons and in addition to more recent methods, we tried to reproduce the original results and extent them to further members of Pospiviroidae which were unknown in 1985. Indeed, individual members of Pospiviroidae consist of a patchwork of sequence fragments from the family but the lengths of fragments do not point to consistent points of rearrangement, which is in conflict with the original hypothesis of fixed domain borders.
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Harada LK, Silva EC, Rossi FP, Cieza B, Oliveira TJ, Pereira C, Tomazetto G, Silva BB, Squina FM, Vila MM, Setubal JC, Ha T, da Silva AM, Balcão VM. Characterization and in vitro testing of newly isolated lytic bacteriophages for the biocontrol of Pseudomonas aeruginosa. Future Microbiol 2022; 17:111-141. [PMID: 34989245 DOI: 10.2217/fmb-2021-0027] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Aim: Two lytic phages were isolated using P. aeruginosa DSM19880 as host and fully characterized. Materials & methods: Phages were characterized physicochemically, biologically and genomically. Results & conclusion: Host range analysis revealed that the phages also infect some multidrug-resistant (MDR) P. aeruginosa clinical isolates. Increasing MOI from 1 to 1000 significantly increased phage efficiency and retarded bacteria regrowth, but phage ph0034 (reduction of 7.5 log CFU/ml) was more effective than phage ph0031 (reduction of 5.1 log CFU/ml) after 24 h. Both phages belong to Myoviridae family. Genome sequencing of phages ph0031 and ph0034 showed that they do not carry toxin, virulence, antibiotic resistance and integrase genes. The results obtained are highly relevant in the actual context of bacterial resistance to antibiotics.
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Affiliation(s)
- Liliam K Harada
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil
| | - Erica C Silva
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil
| | - Fernando Pn Rossi
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Basilio Cieza
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Thais J Oliveira
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil
| | - Carla Pereira
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Geizecler Tomazetto
- Department of Engineering, Biological & Chemical Engineering Section (BCE), Aarhus University, Aarhus, Denmark
| | - Bianca B Silva
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil
| | - Fabio M Squina
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil
| | - Marta Mdc Vila
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil
| | - João C Setubal
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Taekjip Ha
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Aline M da Silva
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Victor M Balcão
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil.,Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
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Development of a Genomics-Based Approach To Identify Putative Hypervirulent Nontyphoidal Salmonella Isolates: Salmonella enterica Serovar Saintpaul as a Model. mSphere 2022; 7:e0073021. [PMID: 34986312 PMCID: PMC8731237 DOI: 10.1128/msphere.00730-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
While differences in human virulence have been reported across nontyphoidal Salmonella (NTS) serovars and associated subtypes, a rational and scalable approach to identify Salmonella subtypes with differential ability to cause human diseases is not available. Here, we used NTS serovar Saintpaul (S. Saintpaul) as a model to determine if metadata and associated whole-genome sequence (WGS) data in the NCBI Pathogen Detection (PD) database can be used to identify (i) subtypes with differential likelihoods of causing human diseases and (ii) genes and single nucleotide polymorphisms (SNPs) potentially responsible for such differences. S. Saintpaul SNP clusters (n = 211) were assigned different epidemiology types (epi-types) based on statistically significant over- or underrepresentation of human clinical isolates, including human associated (HA; n = 29), non-human associated (NHA; n = 23), and other (n = 159). Comparative genomic analyses identified 384 and 619 genes overrepresented among isolates in 5 HA and 4 NHA SNP clusters most significantly associated with the respective isolation source. These genes included 5 HA-associated virulence genes previously reported to be present on Gifsy-1/Gifsy-2 prophages. Additionally, premature stop codons in 3 and 7 genes were overrepresented among the selected HA and NHA SNP clusters, respectively. Tissue culture experiments with strains representing 4 HA and 3 NHA SNP clusters did not reveal evidence for enhanced invasion or intracellular survival for HA strains. However, the presence of sodCI (encoding a superoxide dismutase), found in 4 HA and 1 NHA SNP clusters, was positively correlated with intracellular survival in macrophage-like cells. Post hoc analyses also suggested a possible difference in intracellular survival among S. Saintpaul lineages. IMPORTANCE Not all Salmonella isolates are equally likely to cause human disease, and Salmonella control strategies may unintentionally focus on serovars and subtypes with high prevalence in source populations but are rarely associated with human clinical illness. We describe a framework leveraging WGS data in the NCBI PD database to identify Salmonella subtypes over- and underrepresented among human clinical cases. While we identified genomic signatures associated with HA/NHA SNP clusters, tissue culture experiments failed to identify consistent phenotypic characteristics indicative of enhanced human virulence of HA strains. Our findings illustrate the challenges of defining hypo- and hypervirulent S. Saintpaul and potential limitations of phenotypic assays when evaluating human virulence, for which in vivo experiments are essential. Identification of sodCI, an HA-associated virulence gene associated with enhanced intracellular survival, however, illustrates the potential of the framework and is consistent with prior work identifying specific genomic features responsible for enhanced or reduced virulence of nontyphoidal Salmonella.
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Falkenhagen A, Tausch SH, Labutin A, Grützke J, Heckel G, Ulrich RG, Johne R. OUP accepted manuscript. Virus Evol 2022; 8:veac004. [PMID: 35169491 PMCID: PMC8838746 DOI: 10.1093/ve/veac004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/16/2021] [Accepted: 01/25/2022] [Indexed: 11/14/2022] Open
Abstract
Species A rotaviruses (RVAs) are important aetiological agents of severe diarrhoea in young children. They are also widely distributed in mammals and birds, and increasing evidence indicates the possibility of zoonotic transmission of RVA strains between animals and humans. Moreover, reassortment of the eleven segments of the RVA genome can result in rapid biological changes and may influence pathogenic properties. Here, the nearly complete genome of an RVA strain from a common shrew (Sorex araneus) was sequenced, which showed high nucleotide sequence similarity to additionally determined partial sequences from common shrew RVAs but only very low identity (below 68 per cent) to RVAs from other animal species and humans. New genotypes were assigned to most genome segments of the novel common shrew RVA strain KS14/269, resulting in the genome constellation G39-P[55]-I27-R26-C22-M22-A37-N26-T26-E30-H26. Phylogenetic analyses clustered the common shrew RVAs as ancestral branches of other mammalian and avian RVAs for most of the genome segments, which is in contrast to the phylogeny of the hosts. Nevertheless, conserved sequences typical for all RVAs were identified at the 5ʹ- and 3ʹ- non-coding segment termini. To explore whether the common shrew RVA can exchange genetic material with other mammalian RVAs by reassortment, a reverse genetics system based on the simian RVA strain SA11 was used. However, no viable reassortants could be rescued by exchanging the VP4-, VP6-, or VP7-encoding genome segment alone or in combinations. It can be concluded that highly divergent RVAs are present in common shrews, indicating an evolution of these viruses largely separated from other mammalian and avian RVAs. The zoonotic potential of the virus seems to be low but needs to be further analysed in future.
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Affiliation(s)
- Alexander Falkenhagen
- Department of Biological Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, Berlin 10589, Germany
| | - Simon H Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, Berlin 10589, Germany
| | - Anton Labutin
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, Bern CH-3012, Switzerland
| | - Josephine Grützke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, Berlin 10589, Germany
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, Bern CH-3012, Switzerland
| | - Rainer G Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Südufer 10, Greifswald-Insel Riems 17493, Germany
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Phutela R, Gulati S, Kumar M, Maiti S, Chakraborty D. FnCas9 Editor Linked Uniform Detection Assay for COVID-19. Methods Mol Biol 2022; 2511:149-159. [PMID: 35838958 DOI: 10.1007/978-1-0716-2395-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The recent COVID-19 outbreak and pandemic of 2020 and its surveillance were implemented by quickly adapting the existing diagnostic methods to detect the SARS-CoV-2 RNA. While traditional methods for detecting pathogenic DNA and RNA have relied heavily on gold standard quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and sequencing-based methods, their shortcomings under resource-limited settings have emphasized the need of developing point-of-care (POC) diagnostics. Clustered regularly interspaced short palindromic repeats (CRISPR)-based detection systems provide a rapid and accurate alternative. Here, we describe a CRISPR-Cas9-based detection system FnCas9 Editor Linked Uniform Detection Assay (FELUDA) using a lateral flow test that can detect nucleobase and nucleotide sequences depending upon the stoichiometric-based binding of FnCas9 ribonucleoprotein complex (RNP)-target sequences. The assay has been optimized to be conducted within 1 h and shows 100% sensitivity and 97% specificity in clinical samples across a range of viral loads. The lateral strip results are read using the True Outcome Predicted via Strip Evaluation (TOPSE) smartphone application. This assay is versatile and can be optimized and adjusted to target various diseases.
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Affiliation(s)
- Rhythm Phutela
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India
| | - Sneha Gulati
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India
| | - Manoj Kumar
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India
| | - Souvik Maiti
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India
| | - Debojyoti Chakraborty
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India.
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Monaco DR, Kottapalli SV, Breitwieser FP, Anderson DE, Wijaya L, Tan K, Chia WN, Kammers K, Caturegli P, Waugh K, Roederer M, Petri M, Goldman DW, Rewers M, Wang LF, Larman HB. Deconvoluting virome-wide antibody epitope reactivity profiles. EBioMedicine 2022; 75:103747. [PMID: 34922324 PMCID: PMC8688874 DOI: 10.1016/j.ebiom.2021.103747] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Comprehensive characterization of exposures and immune responses to viral infections is critical to a basic understanding of human health and disease. We previously developed the VirScan system, a programmable phage-display technology for profiling antibody binding to a library of peptides designed to span the human virome. Previous VirScan analytical approaches did not carefully account for antibody cross-reactivity among sequences shared by related viruses or for the disproportionate representation of individual viruses in the library. METHODS Here we present the AntiViral Antibody Response Deconvolution Algorithm (AVARDA), a multi-module software package for analyzing VirScan datasets. AVARDA provides a probabilistic assessment of infection with species-level resolution by considering sequence alignment of all library peptides to each other and to all human viruses. We employed AVARDA to analyze VirScan data from a cohort of encephalitis patients with either known viral infections or undiagnosed etiologies. We further assessed AVARDA's utility in associating viral infection with type 1 diabetes and lupus. FINDINGS By comparing acute and convalescent sera, AVARDA successfully confirmed or detected encephalitis-associated responses to human herpesviruses 1, 3, 4, 5, and 6, improving the rate of diagnosing viral encephalitis in this cohort by 44%. AVARDA analyses of VirScan data from the type 1 diabetes and lupus cohorts implicated enterovirus and herpesvirus infections, respectively. INTERPRETATION AVARDA, in combination with VirScan and other pan-pathogen serological techniques, is likely to find broad utility in the epidemiology and diagnosis of infectious diseases. FUNDING This work was made possible by support from the National Institutes of Health (NIH), the US Army Research Office, the Singapore Infectious Diseases Initiative (SIDI), the Singapore Ministry of Health's National Medical Research Council (NMRC) and the Singapore National Research Foundation (NRF).
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Affiliation(s)
- Daniel R Monaco
- Department of Pathology, Division of Immunology, Institute of Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Sanjay V Kottapalli
- Department of Pathology, Division of Immunology, Institute of Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Florian P Breitwieser
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - Limin Wijaya
- Department of Infectious Diseases, Singapore General Hospital, 20 College Road, 169856, Singapore
| | - Kevin Tan
- National Neuroscience Institute, 11 Jalan Tan Tock Seng, 308433, Singapore
| | - Wan Ni Chia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - Kai Kammers
- Department of Oncology, Division of Biostatistics and Bioinformatics, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Patrizio Caturegli
- Department of Pathology, Division of Immunology, Institute of Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Kathleen Waugh
- Barbara Davis Center for Diabetes, University of Colorado Denver, Aurora, CO, USA
| | - Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michelle Petri
- Department of Medicine, Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel W Goldman
- Department of Medicine, Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marian Rewers
- Barbara Davis Center for Diabetes, University of Colorado Denver, Aurora, CO, USA
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - H Benjamin Larman
- Department of Pathology, Division of Immunology, Institute of Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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125
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Shen L, Liu F, Huang L, Liu G, Zhou L, Peng L. VDA-RWLRLS: An anti-SARS-CoV-2 drug prioritizing framework combining an unbalanced bi-random walk and Laplacian regularized least squares. Comput Biol Med 2022; 140:105119. [PMID: 34902608 PMCID: PMC8664497 DOI: 10.1016/j.compbiomed.2021.105119] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 11/08/2021] [Accepted: 12/02/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND A new coronavirus disease named COVID-19, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is rapidly spreading worldwide. However, there is currently no effective drug to fight COVID-19. METHODS In this study, we developed a Virus-Drug Association (VDA) identification framework (VDA-RWLRLS) combining unbalanced bi-Random Walk, Laplacian Regularized Least Squares, molecular docking, and molecular dynamics simulation to find clues for the treatment of COVID-19. First, virus similarity and drug similarity are computed based on genomic sequences, chemical structures, and Gaussian association profiles. Second, an unbalanced bi-random walk is implemented on the virus network and the drug network, respectively. Third, the results of the random walks are taken as the input of Laplacian regularized least squares to compute the association score for each virus-drug pair. Fourth, the final associations are characterized by integrating the predictions from the virus network and the drug network. Finally, molecular docking and molecular dynamics simulation are implemented to measure the potential of screened anti-COVID-19 drugs and further validate the predicted results. RESULTS In comparison with six state-of-the-art association prediction models (NGRHMDA, SMiR-NBI, LRLSHMDA, VDA-KATZ, VDA-RWR, and VDA-BiRW), VDA-RWLRLS demonstrates superior VDA prediction performance. It obtains the best AUCs of 0.885 8, 0.835 5, and 0.862 5 on the three VDA datasets. Molecular docking and dynamics simulations demonstrated that remdesivir and ribavirin may be potential anti-COVID-19 drugs. CONCLUSIONS Integrating unbalanced bi-random walks, Laplacian regularized least squares, molecular docking, and molecular dynamics simulation, this work initially screened a few anti-SARS-CoV-2 drugs and may contribute to preventing COVID-19 transmission.
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Affiliation(s)
- Ling Shen
- School of Computer Science, Hunan University of Technology, Zhuzhou, 412 007, Hunan, China
| | - Fuxing Liu
- School of Computer Science, Hunan University of Technology, Zhuzhou, 412 007, Hunan, China
| | - Li Huang
- Academy of Arts and Design, Tsinghua University, Beijing, 10 084, Beijing, China; The Future Laboratory, Tsinghua University, Beijing, 10 084, Beijing, China
| | - Guangyi Liu
- School of Computer Science, Hunan University of Technology, Zhuzhou, 412 007, Hunan, China
| | - Liqian Zhou
- School of Computer Science, Hunan University of Technology, Zhuzhou, 412 007, Hunan, China.
| | - Lihong Peng
- School of Computer Science, Hunan University of Technology, Zhuzhou, 412 007, Hunan, China; College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, 412 007, Hunan, China.
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Anderson TK, Inderski B, Diel DG, Hause BM, Porter EG, Clement T, Nelson EA, Bai J, Christopher-Hennings J, Gauger PC, Zhang J, Harmon KM, Main R, Lager KM, Faaberg KS. The United States Swine Pathogen Database: integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine. Database (Oxford) 2021; 2021:6462938. [PMID: 35165687 PMCID: PMC8903347 DOI: 10.1093/database/baab078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 11/04/2021] [Accepted: 11/29/2021] [Indexed: 11/12/2022]
Abstract
Veterinary diagnostic laboratories derive thousands of nucleotide sequences from clinical samples of swine pathogens such as porcine reproductive and respiratory syndrome virus (PRRSV), Senecavirus A and swine enteric coronaviruses. In addition, next generation sequencing has resulted in the rapid production of full-length genomes. Presently, sequence data are released to diagnostic clients but are not publicly available as data may be associated with sensitive information. However, these data can be used for field-relevant vaccines; determining where and when pathogens are spreading; have relevance to research in molecular and comparative virology; and are a component in pandemic preparedness efforts. We have developed a centralized sequence database that integrates private clinical data using PRRSV data as an exemplar, alongside publicly available genomic information. We implemented the Tripal toolkit, a collection of Drupal modules that are used to manage, visualize and disseminate biological data stored within the Chado database schema. New sequences sourced from diagnostic laboratories contain: genomic information; date of collection; collection location; and a unique identifier. Users can download annotated genomic sequences using a customized search interface that incorporates data mined from published literature; search for similar sequences using BLAST-based tools; and explore annotated reference genomes. Additionally, custom annotation pipelines have determined species, the location of open reading frames and nonstructural proteins and the occurrence of putative frame shifts. Eighteen swine pathogens have been curated. The database provides researchers access to sequences discovered by veterinary diagnosticians, allowing for epidemiological and comparative virology studies. The result will be a better understanding on the emergence of novel swine viruses and how these novel strains are disseminated in the USA and abroad. Database URLhttps://swinepathogendb.org.
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Affiliation(s)
- Tavis K Anderson
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, 1920 Dayton Avenue, Ames, IA 50010, USA
| | - Blake Inderski
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, 1920 Dayton Avenue, Ames, IA 50010, USA
| | - Diego G Diel
- Department of Veterinary & Biomedical Sciences, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA.,South Dakota Animal Disease Research & Diagnostic Laboratory, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA.,Diego G. Diel, Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Benjamin M Hause
- Department of Veterinary & Biomedical Sciences, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA.,South Dakota Animal Disease Research & Diagnostic Laboratory, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA
| | - Elizabeth G Porter
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA.,Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA
| | - Travis Clement
- Department of Veterinary & Biomedical Sciences, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA.,South Dakota Animal Disease Research & Diagnostic Laboratory, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA
| | - Eric A Nelson
- Department of Veterinary & Biomedical Sciences, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA.,South Dakota Animal Disease Research & Diagnostic Laboratory, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA
| | - Jianfa Bai
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA.,Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA
| | - Jane Christopher-Hennings
- Department of Veterinary & Biomedical Sciences, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA.,South Dakota Animal Disease Research & Diagnostic Laboratory, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA
| | - Phillip C Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA.,Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Jianqiang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA.,Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Karen M Harmon
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA.,Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Rodger Main
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA.,Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Kelly M Lager
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, 1920 Dayton Avenue, Ames, IA 50010, USA
| | - Kay S Faaberg
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, 1920 Dayton Avenue, Ames, IA 50010, USA
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Dutta K, Elmezayen AD, Al-Obaidi A, Zhu W, Morozova OV, Shityakov S, Khalifa I. Seq12, Seq12m, and Seq13m, peptide analogues of the spike glycoprotein shows antiviral properties against SARS-CoV-2: An in silico study through molecular docking, molecular dynamics simulation, and MM-PB/GBSA calculations. J Mol Struct 2021; 1246:131113. [PMID: 34305174 PMCID: PMC8283670 DOI: 10.1016/j.molstruc.2021.131113] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/10/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023]
Abstract
At the very beginning of the new decade, the COVID-19 pandemic has badly hit modern human societies. SARS-CoV-2, the causative agent of COVID-19 acquiring mutations and circulating as new variants. Herein, we have found three new antiviral peptides (AVPs) against the SARS-CoV-2. These AVPs are analogous to the spike glycoprotein of the SARS-CoV-2. Antiviral peptides, i.e., Seq12, Seq12m, and Seq13m, can block the receptor-binding domain (RBD) of the SARS-CoV-2, which is necessary for communicating with the angiotensin-converting enzyme 2 (ACE2). Also, these AVPs sustain their antiviral properties, even after the insertion of 25 mutations in the RBD (Rosetta and FoldX based). Further, Seq12 and Seq12m showed negligible cytotoxicity. Besides, the binding free energies calculated using MM-PB/GBSA method are also in agreement with the molecular docking studies. The molecular interactions between AVPs and the viral membrane protein (M) also showed a favorable interaction suggesting it could inhibit the viral re-packaging process. In conclusion, this study suggests Seq12, Seq12m, and Seq13m could be helpful to fight against SARS-CoV-2. These AVPs could also aid virus diagnostic tools and nasal spray against SARS-CoV-2 in the future.
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Affiliation(s)
- Kunal Dutta
- Department of Human Physiology, Vidyasagar University, Midnapore 721102, West Bengal, India
| | - Ammar D Elmezayen
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Cibali 34083, Istanbul, Turkey
| | - Anas Al-Obaidi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Cibali 34083, Istanbul, Turkey
| | - Wei Zhu
- College of Food Science and Technology, Huazhong Agricultural University, Key Laboratory of Environment Correlative Food Science, Ministry of Education, Wuhan 430070, China
| | - Olga V Morozova
- I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, 71 Malaya Yamskaya Str., Nizhny Novgorod 603950, Russian Federation
| | - Sergey Shityakov
- Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, 191002 Saint-Petersburg, Russian Federation
| | - Ibrahim Khalifa
- Food Technology Department, Faculty of Agriculture, Moshtohor 13736, Benha University, Egypt
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128
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Gorbalenya AE, Lauber C. Bioinformatics of virus taxonomy: foundations and tools for developing sequence-based hierarchical classification. Curr Opin Virol 2021; 52:48-56. [PMID: 34883443 DOI: 10.1016/j.coviro.2021.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/22/2021] [Accepted: 11/04/2021] [Indexed: 11/03/2022]
Abstract
The genome sequence is the only characteristic readily obtainable for all known viruses, underlying the growing role of comparative genomics in organizing knowledge about viruses in a systematic evolution-aware way, known as virus taxonomy. Overseen by the International Committee on Taxonomy of Viruses (ICTV), development of virus taxonomy involves taxa demarcation at 15 ranks of a hierarchical classification, often in host-specific manner. Outside the ICTV remit, researchers assess fitting numerous unclassified viruses into the established taxa. They employ different metrics of virus clustering, basing on conserved domain(s), separation of viruses in rooted phylogenetic trees and pair-wise distance space. Computational approaches differ further in respect to methodology, number of ranks considered, sensitivity to uneven virus sampling, and visualization of results. Advancing and using computational tools will be critical for improving taxa demarcation across the virosphere and resolving rank origins in research that may also inform experimental virology.
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Affiliation(s)
- Alexander E Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands; Faculty of Bioengineering and Bioinformatics and Belozersky, Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899, Moscow, Russia.
| | - Chris Lauber
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, A Joint Venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
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129
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Vendrell-Mir P, Perroud PF, Haas FB, Meyberg R, Charlot F, Rensing SA, Nogué F, Casacuberta JM. A vertically transmitted amalgavirus is present in certain accessions of the bryophyte Physcomitrium patens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1786-1797. [PMID: 34687260 DOI: 10.1111/tpj.15545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/16/2021] [Indexed: 06/13/2023]
Abstract
In the last few years, next-generation sequencing techniques have started to be used to identify new viruses infecting plants. This has allowed to rapidly increase our knowledge on viruses other than those causing symptoms in economically important crops. Here we used this approach to identify a virus infecting Physcomitrium patens that has the typical structure of the double-stranded RNA endogenous viruses of the Amalgaviridae family, which we named Physcomitrium patens amalgavirus 1, or PHPAV1. PHPAV1 is present only in certain accessions of P. patens, where its RNA can be detected throughout the cell cycle of the plant. Our analysis demonstrates that PHPAV1 can be vertically transmitted through both paternal and maternal germlines, in crosses between accessions that contain the virus with accessions that do not contain it. This work suggests that PHPAV1 can replicate in genomic backgrounds different from those that actually contain the virus and opens the door for future studies on virus-host coevolution.
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Affiliation(s)
- Pol Vendrell-Mir
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, Barcelona, 08193, Spain
| | - Pierre-François Perroud
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Fabian B Haas
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Rabea Meyberg
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Florence Charlot
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Stefan A Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Josep M Casacuberta
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, Barcelona, 08193, Spain
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130
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Baker JJ, Mathy CJP, Schaletzky J. A proposed workflow for proactive virus surveillance and prediction of variants for vaccine design. PLoS Comput Biol 2021; 17:e1009624. [PMID: 34914686 PMCID: PMC8675697 DOI: 10.1371/journal.pcbi.1009624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Jordan J. Baker
- Joint Graduate Program in Bioengineering, University of California, Berkeley and University of California, San Francisco, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, United States of America
| | - Christopher J. P. Mathy
- Joint Graduate Program in Bioengineering, University of California, Berkeley and University of California, San Francisco, Berkeley, California, United States of America
| | - Julia Schaletzky
- Center for Emerging and Neglected Diseases, Immunotherapy and Vaccine Research Initiative, University of California, Berkeley, Berkeley, California, United States of America
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131
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Sayers EW, Cavanaugh M, Clark K, Pruitt KD, Schoch CL, Sherry S, Karsch-Mizrachi I. GenBank. Nucleic Acids Res 2021; 50:D161-D164. [PMID: 34850943 PMCID: PMC8690257 DOI: 10.1093/nar/gkab1135] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/20/2021] [Accepted: 11/08/2021] [Indexed: 11/14/2022] Open
Abstract
GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains 15.3 trillion base pairs from over 2.5 billion nucleotide sequences for 504 000 formally described species. Recent updates include resources for data from the SARS-CoV-2 virus, including a SARS-CoV-2 landing page, NCBI Datasets, NCBI Virus and the Submission Portal. We also discuss upcoming changes to GI identifiers, a new data management interface for BioProject, and advice for providing contextual metadata in submissions.
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Affiliation(s)
- Eric W Sayers
- To whom correspondence should be addressed. Tel: +1 301 496 2475; Fax: +1 301 480 9241;
| | - Mark Cavanaugh
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600RockvillePike, Bethesda, MD 20894, USA
| | - Karen Clark
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600RockvillePike, Bethesda, MD 20894, USA
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600RockvillePike, Bethesda, MD 20894, USA
| | - Conrad L Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600RockvillePike, Bethesda, MD 20894, USA
| | - Stephen T Sherry
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600RockvillePike, Bethesda, MD 20894, USA
| | - Ilene Karsch-Mizrachi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600RockvillePike, Bethesda, MD 20894, USA
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132
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Yap CX, Henders AK, Alvares GA, Wood DLA, Krause L, Tyson GW, Restuadi R, Wallace L, McLaren T, Hansell NK, Cleary D, Grove R, Hafekost C, Harun A, Holdsworth H, Jellett R, Khan F, Lawson LP, Leslie J, Frenk ML, Masi A, Mathew NE, Muniandy M, Nothard M, Miller JL, Nunn L, Holtmann G, Strike LT, de Zubicaray GI, Thompson PM, McMahon KL, Wright MJ, Visscher PM, Dawson PA, Dissanayake C, Eapen V, Heussler HS, McRae AF, Whitehouse AJO, Wray NR, Gratten J. Autism-related dietary preferences mediate autism-gut microbiome associations. Cell 2021; 184:5916-5931.e17. [PMID: 34767757 DOI: 10.1016/j.cell.2021.10.015] [Citation(s) in RCA: 161] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 06/14/2021] [Accepted: 10/13/2021] [Indexed: 12/24/2022]
Abstract
There is increasing interest in the potential contribution of the gut microbiome to autism spectrum disorder (ASD). However, previous studies have been underpowered and have not been designed to address potential confounding factors in a comprehensive way. We performed a large autism stool metagenomics study (n = 247) based on participants from the Australian Autism Biobank and the Queensland Twin Adolescent Brain project. We found negligible direct associations between ASD diagnosis and the gut microbiome. Instead, our data support a model whereby ASD-related restricted interests are associated with less-diverse diet, and in turn reduced microbial taxonomic diversity and looser stool consistency. In contrast to ASD diagnosis, our dataset was well powered to detect microbiome associations with traits such as age, dietary intake, and stool consistency. Overall, microbiome differences in ASD may reflect dietary preferences that relate to diagnostic features, and we caution against claims that the microbiome has a driving role in ASD.
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Affiliation(s)
- Chloe X Yap
- Mater Research Institute, The University of Queensland, Woolloongabba, Queensland 4102, Australia; Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Anjali K Henders
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Gail A Alvares
- Telethon Kids Institute, The University of Western Australia, Nedlands, Western Australia 6009, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - David L A Wood
- Microba Life Sciences, Brisbane, Queensland 4000, Australia
| | - Lutz Krause
- Microba Life Sciences, Brisbane, Queensland 4000, Australia
| | - Gene W Tyson
- Microba Life Sciences, Brisbane, Queensland 4000, Australia; Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland 4102, Australia
| | - Restuadi Restuadi
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Leanne Wallace
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Tiana McLaren
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Narelle K Hansell
- Queensland Brain Institute, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Dominique Cleary
- Telethon Kids Institute, The University of Western Australia, Nedlands, Western Australia 6009, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Rachel Grove
- Faculty of Health, University of Technology Sydney, Sydney, New South Wales 2007, Australia; School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales 2052, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Claire Hafekost
- Telethon Kids Institute, The University of Western Australia, Nedlands, Western Australia 6009, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Alexis Harun
- Telethon Kids Institute, The University of Western Australia, Nedlands, Western Australia 6009, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Helen Holdsworth
- Mater Research Institute, The University of Queensland, Woolloongabba, Queensland 4102, Australia; Child Health Research Centre, The University of Queensland, South Brisbane, Queensland 4101, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Rachel Jellett
- Olga Tennison Autism Research Centre, La Trobe University, Bundoora, Victoria 3086, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Feroza Khan
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales 2052, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Lauren P Lawson
- Olga Tennison Autism Research Centre, La Trobe University, Bundoora, Victoria 3086, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Jodie Leslie
- Telethon Kids Institute, The University of Western Australia, Nedlands, Western Australia 6009, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Mira Levis Frenk
- Mater Research Institute, The University of Queensland, Woolloongabba, Queensland 4102, Australia; Child Health Research Centre, The University of Queensland, South Brisbane, Queensland 4101, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Anne Masi
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales 2052, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Nisha E Mathew
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales 2052, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Melanie Muniandy
- Olga Tennison Autism Research Centre, La Trobe University, Bundoora, Victoria 3086, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Michaela Nothard
- Mater Research Institute, The University of Queensland, Woolloongabba, Queensland 4102, Australia; Child Health Research Centre, The University of Queensland, South Brisbane, Queensland 4101, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Jessica L Miller
- Queensland Brain Institute, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Lorelle Nunn
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Gerald Holtmann
- Faculty of Medicine and Faculty of Health and Behavioural Science, University of Queensland, St Lucia, Queensland 4072, Australia; Department of Gastroenterology & Hepatology, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Lachlan T Strike
- Queensland Brain Institute, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Greig I de Zubicaray
- School of Psychology and Counselling, Faculty of Health, Queensland University of Technology, Kelvin Grove, Queensland 4059, Australia
| | - Paul M Thompson
- Imaging Genetics Center, Mark & Mary Stevens Institute for Neuroimaging & Informatics, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Katie L McMahon
- School of Clinical Sciences, Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Margaret J Wright
- Queensland Brain Institute, The University of Queensland, St Lucia, Queensland 4072, Australia; Centre for Advanced Imaging, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Paul A Dawson
- Mater Research Institute, The University of Queensland, Woolloongabba, Queensland 4102, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Cheryl Dissanayake
- Olga Tennison Autism Research Centre, La Trobe University, Bundoora, Victoria 3086, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Valsamma Eapen
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales 2052, Australia; Academic Unit of Child Psychiatry South West Sydney, Ingham Institute, Liverpool Hospital, Sydney, New South Wales, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Helen S Heussler
- Child Health Research Centre, The University of Queensland, South Brisbane, Queensland 4101, Australia; Child Development Program, Children's Health Queensland, South Brisbane, Queensland 4101, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Andrew J O Whitehouse
- Telethon Kids Institute, The University of Western Australia, Nedlands, Western Australia 6009, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia; Queensland Brain Institute, The University of Queensland, St Lucia, Queensland 4072, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Jacob Gratten
- Mater Research Institute, The University of Queensland, Woolloongabba, Queensland 4102, Australia; Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia.
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133
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Brahma A, Leon RG, Hernandez GL, Wurm Y. Larger, more connected societies of ants have a higher prevalence of viruses. Mol Ecol 2021; 31:859-865. [PMID: 34800339 DOI: 10.1111/mec.16284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 11/28/2022]
Abstract
The benefits of cooperative living for foraging, nesting, defence and buffering environmental challenges lead animals with the most highly social lifestyles to dominate many ecosystems. However, living in larger, more highly connected groups should also increase the risks of pathogen exposure and transmission. While over long timescales selective responses could buffer the impacts of potential higher pathogen prevalence, similar processes are unlikely over short timescales. The red fire ant Solenopsis invicta is ideal for measuring the effects of group size on pathogen prevalence because two types of society coexist in this species: smaller single-nest single-queen colonies that are highly aggressive to their neighbours and larger multiple-queen colonies that exchange resources with neighbouring nests. We compare the presence of viruses between these two colony types using metagenomic sequence classification of RNA-sequencing reads. We find that queens from multiple-queen colonies have 8.3-times higher viral load and 1.5-times higher viral diversity than queens from single-queen colonies. This finding characterizes a rarely considered cost of transitions to more highly social living. Furthermore, our results show that highly social invertebrates can harbour many viruses.
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Affiliation(s)
- Anindita Brahma
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Raphael Gray Leon
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.,University College London, London, UK
| | - Gabriel Luis Hernandez
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Yannick Wurm
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.,Alan Turing Institute, London, UK
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134
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Computational methods for inferring location and genealogy of overlapping genes in virus genomes: approaches and applications. Curr Opin Virol 2021; 52:1-8. [PMID: 34798370 PMCID: PMC8594276 DOI: 10.1016/j.coviro.2021.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/02/2022]
Abstract
Viruses may evolve to increase the amount of encoded genetic information by means of overlapping genes, which utilize several reading frames. Such overlapping genes may be especially impactful for genomes of small size, often serving a source of novel accessory proteins, some of which play a crucial role in viral pathogenicity or in promoting the systemic spread of virus. Diverse genome-based metrics were proposed to facilitate recognition of overlapping genes that otherwise may be overlooked during genome annotation. They can detect the atypical codon bias associated with the overlap (e.g. a statistically significant reduction in variability at synonymous sites) or other sequence-composition features peculiar to overlapping genes. In this review, I compare nine computational methods, discuss their strengths and limitations, and survey how they were applied to detect candidate overlapping genes in the genome of SARS-CoV-2, the etiological agent of COVID-19 pandemic.
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135
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Friedrich I, Bodenberger B, Neubauer H, Hertel R, Daniel R. Down in the pond: Isolation and characterization of a new Serratia marcescens strain (LVF3) from the surface water near frog's lettuce (Groenlandia densa). PLoS One 2021; 16:e0259673. [PMID: 34748577 PMCID: PMC8575298 DOI: 10.1371/journal.pone.0259673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/22/2021] [Indexed: 11/18/2022] Open
Abstract
Serratia marcescens is a species that belongs to the family of Yersiniaceae. This family comprises taxa representing opportunistic human- and phytopathogens but also plant growth-promoting rhizobacteria (PGPR). This study describes a novel Gram-negative strain (LVF3R) of the species Serratia marcescens. The strain was characterized genomically, morphologically, and physiologically. In addition, the potential of the isolate to act as a host strain to assess the diversity of Serratia associated phages in environmental samples was explored. Average nucleotide identity analysis revealed that LVF3R belongs to the species Serratia marcescens. In silico analysis and ProphageSeq data resulted in the identification of one prophage, which is capable of viral particle formation. Electron microscopy showed cells of a rod-shaped, flagellated morphotype. The cells revealed a length and width of 1-1.6 μm and 0.8 μm, respectively. LVF3R showed optimal growth at 30 C and in the presence of up to 2% (w/v) NaCl. It exhibited resistances to ampicillin, erythromycin, oxacillin, oxytetracycline, rifampicin, tetracycline, and vancomycin. Genome data indicate that strain S. marcescens LVF3R is a potential PGPR strain. It harbors genes coding for indole acetic acid (IAA) biosynthesis, siderophore production, plant polymer degradation enzymes, acetoin synthesis, flagellar proteins, type IV secretion system, chemotaxis, phosphorous solubilization, and biofilm formation.
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Affiliation(s)
- Ines Friedrich
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Bernhard Bodenberger
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Hannes Neubauer
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Robert Hertel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
- FG Synthetic Microbiology, Institute of Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
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136
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Steinbachová L, Matoušek J, Steger G, Matoušková H, Radišek S, Honys D. Transformation of Seed Non-Transmissible Hop Viroids in Nicotiana benthamiana Causes Distortions in Male Gametophyte Development. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112398. [PMID: 34834761 PMCID: PMC8624972 DOI: 10.3390/plants10112398] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/22/2021] [Accepted: 11/03/2021] [Indexed: 05/27/2023]
Abstract
Viroids are small, non-coding, parasitic RNAs that promote developmental distortions in sensitive plants. We analyzed pollen of Nicotiana benthamiana after infection and/or ectopic transformation with cDNAs of citrus bark cracking viroid (CBCVd), apple fruit crinkle viroid (AFCVd) and potato spindle tuber viroid (PSTVd) variant AS1. These viroids were seed non-transmissible in N. benthamiana. All viroids propagated to high levels in immature anthers similar to leaves, while their levels were drastically reduced by approximately 3.6 × 103, 800 and 59 times in mature pollen of CBCVd, AFCVd and PSTVd infected N. benthamiana, respectively, in comparison to leaves. These results suggest similar elimination processes during male gametophyte development as in the Nicotiana tabacum we presented in our previous study. Mature pollen of N. benthamiana showed no apparent defects in infected plants although all three viroids induced strong pathological symptoms on leaves. While Nicotiana species have naturally bicellular mature pollen, we noted a rare occurrence of mature pollen with three nuclei in CBCVd-infected N. benthamiana. Changes in the expression of ribosomal marker proteins in AFCVd-infected pollen were detected, suggesting some changes in pollen metabolism. N. benthamiana transformed with 35S-driven viroid cDNAs showed strong symptoms including defects in pollen development. A large number of aborted pollen (34% and 62%) and a slight increase of young pollen grains (8% and 15%) were found in mature pollen of AFCVd and CBCVd transformants, respectively, in comparison to control plants (3.9% aborted pollen and 0.3% young pollen). Moreover, pollen grains with malformed nuclei or trinuclear pollen were found in CBCVd-transformed plants. Our results suggest that "forcing" overexpression of seed non-transmissible viroid led to strong pollen pathogenesis. Viroid adaptation to pollen metabolism can be assumed as an important factor for viroid transmissibility through pollen and seeds.
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Affiliation(s)
- Lenka Steinbachová
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic;
| | - Jaroslav Matoušek
- Biology Centre of the Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (J.M.); (H.M.)
| | - Gerhard Steger
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, D-40204 Düsseldorf, Germany;
| | - Helena Matoušková
- Biology Centre of the Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (J.M.); (H.M.)
| | - Sebastjan Radišek
- Slovenian Institute of Hop Research and Brewing, Cesta Žalskega tabora 2, SI-3310 Žalec, Slovenia;
| | - David Honys
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic;
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137
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DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes. mBio 2021; 12:e0259521. [PMID: 34724822 PMCID: PMC8567247 DOI: 10.1128/mbio.02595-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Soil viruses are abundant, but the influence of the environment and climate on soil viruses remains poorly understood. Here, we addressed this gap by comparing the diversity, abundance, lifestyle, and metabolic potential of DNA viruses in three grassland soils with historical differences in average annual precipitation, low in eastern Washington (WA), high in Iowa (IA), and intermediate in Kansas (KS). Bioinformatics analyses were applied to identify a total of 2,631 viral contigs, including 14 complete viral genomes from three deep metagenomes (1 terabase [Tb] each) that were sequenced from bulk soil DNA. An additional three replicate metagenomes (∼0.5 Tb each) were obtained from each location for statistical comparisons. Identified viruses were primarily bacteriophages targeting dominant bacterial taxa. Both viral and host diversity were higher in soil with lower precipitation. Viral abundance was also significantly higher in the arid WA location than in IA and KS. More lysogenic markers and fewer clustered regularly interspaced short palindromic repeats (CRISPR) spacer hits were found in WA, reflecting more lysogeny in historically drier soil. More putative auxiliary metabolic genes (AMGs) were also detected in WA than in the historically wetter locations. The AMGs occurring in 18 pathways could potentially contribute to carbon metabolism and energy acquisition in their hosts. Structural equation modeling (SEM) suggested that historical precipitation influenced viral life cycle and selection of AMGs. The observed and predicted relationships between soil viruses and various biotic and abiotic variables have value for predicting viral responses to environmental change.
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138
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Correcting the Estimation of Viral Taxa Distributions in Next-Generation Sequencing Data after Applying Artificial Neural Networks. Genes (Basel) 2021; 12:genes12111755. [PMID: 34828361 PMCID: PMC8624964 DOI: 10.3390/genes12111755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022] Open
Abstract
Estimating the taxonomic composition of viral sequences in a biological samples processed by next-generation sequencing is an important step in comparative metagenomics. Mapping sequencing reads against a database of known viral reference genomes, however, fails to classify reads from novel viruses whose reference sequences are not yet available in public databases. Instead of a mapping approach, and in order to classify sequencing reads at least to a taxonomic level, the performance of artificial neural networks and other machine learning models was studied. Taxonomic and genomic data from the NCBI database were used to sample labelled sequencing reads as training data. The fitted neural network was applied to classify unlabelled reads of simulated and real-world test sets. Additional auxiliary test sets of labelled reads were used to estimate the conditional class probabilities, and to correct the prior estimation of the taxonomic distribution in the actual test set. Among the taxonomic levels, the biological order of viruses provided the most comprehensive data base to generate training data. The prediction accuracy of the artificial neural network to classify test reads to their viral order was considerably higher than that of a random classification. Posterior estimation of taxa frequencies could correct the primary classification results.
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139
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Tang G, Cho M, Wang X. OncoDB: an interactive online database for analysis of gene expression and viral infection in cancer. Nucleic Acids Res 2021; 50:D1334-D1339. [PMID: 34718715 PMCID: PMC8728272 DOI: 10.1093/nar/gkab970] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/08/2021] [Accepted: 10/05/2021] [Indexed: 02/06/2023] Open
Abstract
Large-scale multi-omics datasets, most prominently from the TCGA consortium, have been made available to the public for systematic characterization of human cancers. However, to date, there is a lack of corresponding online resources to utilize these valuable data to study gene expression dysregulation and viral infection, two major causes for cancer development and progression. To address these unmet needs, we established OncoDB, an online database resource to explore abnormal patterns in gene expression as well as viral infection that are correlated to clinical features in cancer. Specifically, OncoDB integrated RNA-seq, DNA methylation, and related clinical data from over 10 000 cancer patients in the TCGA study as well as from normal tissues in the GTEx study. Another unique aspect of OncoDB is its focus on oncoviruses. By mining TCGA RNA-seq data, we have identified six major oncoviruses across cancer types and further correlated viral infection to changes in host gene expression and clinical outcomes. All the analysis results are integratively presented in OncoDB with a flexible web interface to search for data related to RNA expression, DNA methylation, viral infection, and clinical features of the cancer patients. OncoDB is freely accessible at http://oncodb.org.
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Affiliation(s)
- Gongyu Tang
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, USA.,Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, MO, USA
| | - Minsu Cho
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, USA
| | - Xiaowei Wang
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, USA.,University of Illinois Cancer Center, Chicago, IL, USA
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140
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Rajagopala SV, Bakhoum NG, Pakala SB, Shilts MH, Rosas-Salazar C, Mai A, Boone HH, McHenry R, Yooseph S, Halasa N, Das SR. Metatranscriptomics to characterize respiratory virome, microbiome, and host response directly from clinical samples. CELL REPORTS METHODS 2021; 1:100091. [PMID: 34790908 PMCID: PMC8594859 DOI: 10.1016/j.crmeth.2021.100091] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 05/18/2021] [Accepted: 09/10/2021] [Indexed: 12/23/2022]
Abstract
We developed a metatranscriptomics method that can simultaneously capture the respiratory virome, microbiome, and host response directly from low biomass samples. Using nasal swab samples, we capture RNA virome with sufficient sequencing depth required to assemble complete genomes. We find a surprisingly high frequency of respiratory syncytial virus (RSV) and coronavirus (CoV) in healthy children, and a high frequency of RSV-A and RSV-B co-detections in children with symptomatic RSV. In addition, we have identified commensal and pathogenic bacteria and fungi at the species level. Functional analysis revealed that H. influenzae was highly active in symptomatic RSV subjects. The host nasal transcriptome reveled upregulation of the innate immune system, anti-viral response and inflammasome pathway, and downregulation of fatty acid pathways in children with symptomatic RSV. Overall, we demonstrate that our method is broadly applicable to infer the transcriptome landscape of an infected system, surveil respiratory infections, and to sequence RNA viruses directly from clinical samples.
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Affiliation(s)
- Seesandra V. Rajagopala
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nicole G. Bakhoum
- Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Suman B. Pakala
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Meghan H. Shilts
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Christian Rosas-Salazar
- Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Annie Mai
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Helen H. Boone
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Rendie McHenry
- Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Shibu Yooseph
- Department of Computer Science, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL 32816, USA
| | - Natasha Halasa
- Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Suman R. Das
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Otolaryngology and Head and Neck Surgery, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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141
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Müller R, Gerwel TM, Kimuda MP, Bishop ÖT, Veale CGL, Hoppe HC. Virtual screening and in vitro validation identifies the first reported inhibitors of Salmonella enterica HPPK. RSC Med Chem 2021; 12:1750-1756. [PMID: 34778775 PMCID: PMC8528203 DOI: 10.1039/d1md00237f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 08/23/2021] [Indexed: 11/21/2022] Open
Abstract
HPPK, which directly precedes DHPS in the folate biosynthetic pathway, is a promising but chronically under-exploited anti-microbial target. Here we report the identification of new S. enterica HPPK inhibitors, offering potential for new resistance circumventing S. enterica therapies as well as avenues for diversifying the current HPPK inhibitor space.
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Affiliation(s)
- Ronel Müller
- School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal Private Bag X01 Scottsville 3209 South Africa
| | - Tiaan M Gerwel
- Faculty of Pharmacy, Rhodes University Makhanda 6140 South Africa
| | - Magambo Phillip Kimuda
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University Makhanda 6140 South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University Makhanda 6140 South Africa
| | - Clinton G L Veale
- School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal Private Bag X01 Scottsville 3209 South Africa
| | - Heinrich C Hoppe
- Department of Biochemistry and Microbiology, Rhodes University Makhanda 6140 South Africa
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142
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Abstract
Enterovirus D68 (EV-D68) causes a range of clinical manifestations, including asthma-like illness, severe respiratory disease, and acute flaccid myelitis. EV-D68 has caused worldwide outbreaks since 2014 and is now recognized as a reemerging infection in many countries. EV-D68-specific PCR assays are widely used for the diagnosis of EV-D68 infection; however, assay sensitivity is a concern because of genetic changes in recently circulated EV-D68. To address this, we summarized EV-D68 sequences from previously reported world outbreaks from 2014 through 2020 on GenBank, and found several mutations at the primer and probe binding sites of the existing EV-D68-specific PCR assays. Subsequently, we designed two novel assays corresponding to the recently reported EV-D68 sequences: an EV-D68-specific real-time and seminested PCR. In an analysis of 22 EV-D68 confirmed cases during a recent EV-D68 outbreak in Japan, the new real-time PCR had higher sensitivity than the existing assay (100% versus 45%, P < 0.01) and a lower median CT value (27.8 versus 32.8, P = 0.005). Sensitivity was higher for the new nonnested PCR (91%) than for the existing seminested PCR assay (50%, P < 0.01). The specificity of the new real-time PCR was 100% using samples from non-EV-D68-infected cases (n = 135). In conclusion, our novel assays had higher sensitivity than the existing assay and might lead to more accurate diagnosis of recently circulating EV-D68. To prepare for future EV-D68 outbreaks, EV-D68-specific assays must be continuously monitored and updated.
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143
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Diversity and distribution of viruses inhabiting the deepest ocean on Earth. THE ISME JOURNAL 2021; 15:3094-3110. [PMID: 33972725 PMCID: PMC8443753 DOI: 10.1038/s41396-021-00994-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 04/08/2021] [Accepted: 04/20/2021] [Indexed: 02/01/2023]
Abstract
As the most abundant biological entities on the planet, viruses significantly influence the overall functioning of marine ecosystems. The abundance, distribution, and biodiversity of viral communities in the upper ocean have been relatively well studied, but our understanding of viruses in the hadal biosphere remains poor. Here, we established the oceanic trench viral genome dataset (OTVGD) by analysing 19 microbial metagenomes derived from seawater and sediment samples of the Mariana, Yap, and Kermadec Trenches. The trench viral communities harbored remarkably high novelty, and they were predicted to infect ecologically important microbial clades, including Thaumarchaeota and Oleibacter. Significant inter-trench and intra-trench exchange of viral communities was proposed. Moreover, viral communities in different habitats (seawater/sediment and depth-stratified ocean zones) exhibited distinct niche-dependent distribution patterns and genomic properties. Notably, microbes and viruses in the hadopelagic seawater seemed to preferably adopt lysogenic lifestyles compared to those in the upper ocean. Furthermore, niche-specific auxiliary metabolic genes were identified in the hadal viral genomes, and a novel viral D-amino acid oxidase was functionally and phylogenetically characterized, suggesting the contribution of these genes in the utilization of refractory organic matter. Together, these findings highlight the genomic novelty, dynamic movement, and environment-driven diversification of viral communities in oceanic trenches, and suggest that viruses may influence the hadal ecosystem by reprogramming the metabolism of their hosts and modulating the community of keystone microbes.
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144
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Kryukov K, Ueda MT, Nakagawa S, Imanishi T. Sequence Compression Benchmark (SCB) database-A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences. Gigascience 2021; 9:5867695. [PMID: 32627830 PMCID: PMC7336184 DOI: 10.1093/gigascience/giaa072] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 06/01/2020] [Accepted: 06/15/2020] [Indexed: 01/22/2023] Open
Abstract
Background Nearly all molecular sequence databases currently use gzip for data compression. Ongoing rapid accumulation of stored data calls for a more efficient compression tool. Although numerous compressors exist, both specialized and general-purpose, choosing one of them was difficult because no comprehensive analysis of their comparative advantages for sequence compression was available. Findings We systematically benchmarked 430 settings of 48 compressors (including 29 specialized sequence compressors and 19 general-purpose compressors) on representative FASTA-formatted datasets of DNA, RNA, and protein sequences. Each compressor was evaluated on 17 performance measures, including compression strength, as well as time and memory required for compression and decompression. We used 27 test datasets including individual genomes of various sizes, DNA and RNA datasets, and standard protein datasets. We summarized the results as the Sequence Compression Benchmark database (SCB database, http://kirr.dyndns.org/sequence-compression-benchmark/), which allows custom visualizations to be built for selected subsets of benchmark results. Conclusion We found that modern compressors offer a large improvement in compactness and speed compared to gzip. Our benchmark allows compressors and their settings to be compared using a variety of performance measures, offering the opportunity to select the optimal compressor on the basis of the data type and usage scenario specific to a particular application.
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Affiliation(s)
- Kirill Kryukov
- Correspondence address. Kirill Kryukov, Department of Genomics and Evolutionary Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan. E-mail:
| | - Mahoko Takahashi Ueda
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259–1193, Japan
- Current address: Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo, Tokyo 113-8510, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259–1193, Japan
| | - Tadashi Imanishi
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259–1193, Japan
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145
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Ramakrishnan SG, Robert B, Salim A, Ananthan P, Sivaramakrishnan M, Subramaniam S, Natesan S, Suresh R, Rajeshkumar G, Maran JP, Al-Dhabi NA, Karuppiah P, Valan Arasu M. Nanotechnology based solutions to combat zoonotic viruses with special attention to SARS, MERS, and COVID 19: Detection, protection and medication. Microb Pathog 2021; 159:105133. [PMID: 34390768 PMCID: PMC8358084 DOI: 10.1016/j.micpath.2021.105133] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 04/01/2021] [Accepted: 08/09/2021] [Indexed: 12/23/2022]
Abstract
Zoonotic viruses originate from birds or animal sources and responsible for disease transmission from animals to people through zoonotic spill over and presents a significant global health concern due to lack of rapid diagnostics and therapeutics. The Corona viruses (CoV) were known to be transmitted in mammals. Early this year, SARS-CoV-2, a novel strain of corona virus, was identified as the causative pathogen of an outbreak of viral pneumonia in Wuhan, China. The disease later named corona virus disease 2019 (COVID-19), subsequently spread across the globe rapidly. Nano-particles and viruses are comparable in size, which serves to be a major advantage of using nano-material in clinical strategy to combat viruses. Nanotechnology provides novel solutions against zoonotic viruses by providing cheap and efficient detection methods, novel, and new effective rapid diagnostics and therapeutics. The prospective of nanotechnology in COVID 19 is exceptionally high due to their small size, large surface-to-volume ratio, susceptibility to modification, intrinsic viricidal activity. The nano-based strategies address the COVID 19 by extending their role in i) designing nano-materials for drug/vaccine delivery, ii) developing nano-based diagnostic approaches like nano-sensors iii) novel nano-based personal protection equipment to be used in prevention strategies.This review aims to bring attention to the significant contribution of nanotechnology to mitigate against zoonotic viral pandemics by prevention, faster diagnosis and medication point of view.
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Affiliation(s)
- Sankar Ganesh Ramakrishnan
- Bioprocess and Biomaterials laboratory, Department of Microbial Biotechnology, Bharathiar University, Coimbatore, India
| | - Becky Robert
- Bioprocess and Biomaterials laboratory, Department of Microbial Biotechnology, Bharathiar University, Coimbatore, India
| | - Anisha Salim
- Bioprocess and Biomaterials laboratory, Department of Microbial Biotechnology, Bharathiar University, Coimbatore, India
| | - Padma Ananthan
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | | | - Sadhasivam Subramaniam
- Bioprocess and Biomaterials laboratory, Department of Microbial Biotechnology, Bharathiar University, Coimbatore, India; Department of Extension and Career Guidance, Bharathiar University, Coimbatore, India.
| | - Sivarajasekar Natesan
- Unit Operations laboratory, Department of Biotechnology, Kumaraguru College of Technology, Coimbatore, India
| | - Rahul Suresh
- Department of Physics, Bharathiar University, Coimbatore, India
| | - G Rajeshkumar
- Department of Mechanical Engineering, PSG Institute of Technology and Applied Research, Coimbatore, Tamilnadu, India
| | - J Prakash Maran
- Department of Food Science and Nutrition, Periyar University, Salem, Tamilnadu, India.
| | - Naif Abdullah Al-Dhabi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Ponmurugan Karuppiah
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia.
| | - Mariadhas Valan Arasu
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
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146
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Oluniyi PE, Ajogbasile F, Oguzie J, Uwanibe J, Kayode A, Happi A, Ugwu A, Olumade T, Ogunsanya O, Eromon PE, Folarin O, Frost SDW, Heeney J, Happi CT. VGEA: an RNA viral assembly toolkit. PeerJ 2021; 9:e12129. [PMID: 34567846 PMCID: PMC8428259 DOI: 10.7717/peerj.12129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 08/17/2021] [Indexed: 12/11/2022] Open
Abstract
Next generation sequencing (NGS)-based studies have vastly increased our understanding of viral diversity. Viral sequence data obtained from NGS experiments are a rich source of information, these data can be used to study their epidemiology, evolution, transmission patterns, and can also inform drug and vaccine design. Viral genomes, however, represent a great challenge to bioinformatics due to their high mutation rate and forming quasispecies in the same infected host, bringing about the need to implement advanced bioinformatics tools to assemble consensus genomes well-representative of the viral population circulating in individual patients. Many tools have been developed to preprocess sequencing reads, carry-out de novo or reference-assisted assembly of viral genomes and assess the quality of the genomes obtained. Most of these tools however exist as standalone workflows and usually require huge computational resources. Here we present (Viral Genomes Easily Analyzed), a Snakemake workflow for analyzing RNA viral genomes. VGEA enables users to map sequencing reads to the human genome to remove human contaminants, split bam files into forward and reverse reads, carry out de novo assembly of forward and reverse reads to generate contigs, pre-process reads for quality and contamination, map reads to a reference tailored to the sample using corrected contigs supplemented by the user's choice of reference sequences and evaluate/compare genome assemblies. We designed a project with the aim of creating a flexible, easy-to-use and all-in-one pipeline from existing/stand-alone bioinformatics tools for viral genome analysis that can be deployed on a personal computer. VGEA was built on the Snakemake workflow management system and utilizes existing tools for each step: fastp (Chen et al., 2018) for read trimming and read-level quality control, BWA (Li & Durbin, 2009) for mapping sequencing reads to the human reference genome, SAMtools (Li et al., 2009) for extracting unmapped reads and also for splitting bam files into fastq files, IVA (Hunt et al., 2015) for de novo assembly to generate contigs, shiver (Wymant et al., 2018) to pre-process reads for quality and contamination, then map to a reference tailored to the sample using corrected contigs supplemented with the user's choice of existing reference sequences, SeqKit (Shen et al., 2016) for cleaning shiver assembly for QUAST, QUAST (Gurevich et al., 2013) to evaluate/assess the quality of genome assemblies and MultiQC (Ewels et al., 2016) for aggregation of the results from fastp, BWA and QUAST. Our pipeline was successfully tested and validated with SARS-CoV-2 (n = 20), HIV-1 (n = 20) and Lassa Virus (n = 20) datasets all of which have been made publicly available. VGEA is freely available on GitHub at: https://github.com/pauloluniyi/VGEA under the GNU General Public License.
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Affiliation(s)
- Paul E Oluniyi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Fehintola Ajogbasile
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Judith Oguzie
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Jessica Uwanibe
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Adeyemi Kayode
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Anise Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Alphonsus Ugwu
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Testimony Olumade
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Olusola Ogunsanya
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Philomena Ehiaghe Eromon
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Onikepe Folarin
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Simon D W Frost
- Microsoft Research, Redmond, WA, United States of America.,London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Jonathan Heeney
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Christian T Happi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
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147
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Katz KS, Shutov O, Lapoint R, Kimelman M, Brister JR, O’Sullivan C. STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions. Genome Biol 2021; 22:270. [PMID: 34544477 PMCID: PMC8450716 DOI: 10.1186/s13059-021-02490-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/08/2021] [Indexed: 02/03/2024] Open
Abstract
Sequence Read Archive submissions to the National Center for Biotechnology Information often lack useful metadata, which limits the utility of these submissions. We describe the Sequence Taxonomic Analysis Tool (STAT), a scalable k-mer-based tool for fast assessment of taxonomic diversity intrinsic to submissions, independent of metadata. We show that our MinHash-based k-mer tool is accurate and scalable, offering reliable criteria for efficient selection of data for further analysis by the scientific community, at once validating submissions while also augmenting sample metadata with reliable, searchable, taxonomic terms.
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Affiliation(s)
- Kenneth S. Katz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 USA
| | - Oleg Shutov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 USA
| | - Richard Lapoint
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 USA
| | - Michael Kimelman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 USA
| | - J. Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 USA
| | - Christopher O’Sullivan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 USA
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148
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Garneau JR, Legrand V, Marbouty M, Press MO, Vik DR, Fortier LC, Sullivan MB, Bikard D, Monot M. High-throughput identification of viral termini and packaging mechanisms in virome datasets using PhageTermVirome. Sci Rep 2021; 11:18319. [PMID: 34526611 PMCID: PMC8443750 DOI: 10.1038/s41598-021-97867-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 08/27/2021] [Indexed: 11/13/2022] Open
Abstract
Viruses that infect bacteria (phages) are increasingly recognized for their importance in diverse ecosystems but identifying and annotating them in large-scale sequence datasets is still challenging. Although efficient scalable virus identification tools are emerging, defining the exact ends (termini) of phage genomes is still particularly difficult. The proper identification of termini is crucial, as it helps in characterizing the packaging mechanism of bacteriophages and provides information on various aspects of phage biology. Here, we introduce PhageTermVirome (PTV) as a tool for the easy and rapid high-throughput determination of phage termini and packaging mechanisms using modern large-scale metagenomics datasets. We successfully tested the PTV algorithm on a mock virome dataset and then used it on two real virome datasets to achieve the rapid identification of more than 100 phage termini and packaging mechanisms, with just a few hours of computing time. Because PTV allows the identification of free fully formed viral particles (by recognition of termini present only in encapsidated DNA), it can also complement other virus identification softwares to predict the true viral origin of contigs in viral metagenomics datasets. PTV is a novel and unique tool for high-throughput characterization of phage genomes, including phage termini identification and characterization of genome packaging mechanisms. This software should help researchers better visualize, map and study the virosphere. PTV is freely available for downloading and installation at https://gitlab.pasteur.fr/vlegrand/ptv.
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Affiliation(s)
| | - Véronique Legrand
- Infrastructure et Ingénierie Scientifique, Institut Pasteur, 75015, Paris, France
| | - Martial Marbouty
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, 75015, Paris, France
| | | | - Dean R Vik
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
| | - Louis-Charles Fortier
- Faculty of Medicine and Health Sciences, Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
| | - David Bikard
- Département de Microbiologie, Institut Pasteur, Groupe Biologie de Synthèse, 75015, Paris, France
| | - Marc Monot
- Biomics Platform, C2RT, Institut Pasteur, 75015, Paris, France.
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149
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Van Poelvoorde LAE, Bogaerts B, Fu Q, De Keersmaecker SCJ, Thomas I, Van Goethem N, Van Gucht S, Winand R, Saelens X, Roosens N, Vanneste K. Whole-genome-based phylogenomic analysis of the Belgian 2016-2017 influenza A(H3N2) outbreak season allows improved surveillance. Microb Genom 2021; 7. [PMID: 34477544 PMCID: PMC8715427 DOI: 10.1099/mgen.0.000643] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seasonal influenza epidemics are associated with high mortality and morbidity in the human population. Influenza surveillance is critical for providing information to national influenza programmes and for making vaccine composition predictions. Vaccination prevents viral infections, but rapid influenza evolution results in emerging mutants that differ antigenically from vaccine strains. Current influenza surveillance relies on Sanger sequencing of the haemagglutinin (HA) gene. Its classification according to World Health Organization (WHO) and European Centre for Disease Prevention and Control (ECDC) guidelines is based on combining certain genotypic amino acid mutations and phylogenetic analysis. Next-generation sequencing technologies enable a shift to whole-genome sequencing (WGS) for influenza surveillance, but this requires laboratory workflow adaptations and advanced bioinformatics workflows. In this study, 253 influenza A(H3N2) positive clinical specimens from the 2016–2017 Belgian season underwent WGS using the Illumina MiSeq system. HA-based classification according to WHO/ECDC guidelines did not allow classification of all samples. A new approach, considering the whole genome, was investigated based on using powerful phylogenomic tools including beast and Nextstrain, which substantially improved phylogenetic classification. Moreover, Bayesian inference via beast facilitated reassortment detection by both manual inspection and computational methods, detecting intra-subtype reassortants at an estimated rate of 15 %. Real-time analysis (i.e. as an outbreak is ongoing) via Nextstrain allowed positioning of the Belgian isolates into the globally circulating context. Finally, integration of patient data with phylogenetic groups and reassortment status allowed detection of several associations that would have been missed when solely considering HA, such as hospitalized patients being more likely to be infected with A(H3N2) reassortants, and the possibility to link several phylogenetic groups to disease severity indicators could be relevant for epidemiological monitoring. Our study demonstrates that WGS offers multiple advantages for influenza monitoring in (inter)national influenza surveillance, and proposes an improved methodology. This allows leveraging all information contained in influenza genomes, and allows for more accurate genetic characterization and reassortment detection.
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Affiliation(s)
- Laura A E Van Poelvoorde
- Transversal Activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium.,National Influenza Centre, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Bert Bogaerts
- Transversal Activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Department of Information Technology, IDLab, IMEC, Ghent University, Ghent, Belgium
| | - Qiang Fu
- Transversal Activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | | | - Isabelle Thomas
- National Influenza Centre, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | | | - Steven Van Gucht
- National Influenza Centre, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - Raf Winand
- Transversal Activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - Xavier Saelens
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Nancy Roosens
- Transversal Activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
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150
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Guo Q, Li M, Wang C, Guo J, Jiang X, Tan J, Wu S, Wang P, Xiao T, Zhou M, Fang Z, Xiao Y, Zhu H. Predicting hosts based on early SARS-CoV-2 samples and analyzing the 2020 pandemic. Sci Rep 2021; 11:17422. [PMID: 34465838 PMCID: PMC8408148 DOI: 10.1038/s41598-021-96903-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/18/2021] [Indexed: 11/16/2022] Open
Abstract
The SARS-CoV-2 pandemic has raised concerns in the identification of the hosts of the virus since the early stages of the outbreak. To address this problem, we proposed a deep learning method, DeepHoF, based on extracting viral genomic features automatically, to predict the host likelihood scores on five host types, including plant, germ, invertebrate, non-human vertebrate and human, for novel viruses. DeepHoF made up for the lack of an accurate tool, reaching a satisfactory AUC of 0.975 in the five-classification, and could make a reliable prediction for the novel viruses without close neighbors in phylogeny. Additionally, to fill the gap in the efficient inference of host species for SARS-CoV-2 using existing tools, we conducted a deep analysis on the host likelihood profile calculated by DeepHoF. Using the isolates sequenced in the earliest stage of the COVID-19 pandemic, we inferred that minks, bats, dogs and cats were potential hosts of SARS-CoV-2, while minks might be one of the most noteworthy hosts. Several genes of SARS-CoV-2 demonstrated their significance in determining the host range. Furthermore, a large-scale genome analysis, based on DeepHoF's computation for the later pandemic in 2020, disclosed the uniformity of host range among SARS-CoV-2 samples and the strong association of SARS-CoV-2 between humans and minks.
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Affiliation(s)
- Qian Guo
- State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
- Center for Quantitative Biology, Peking University, Beijing, 100871, China
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Mo Li
- Peking University-Tsinghua University-National Institute of Biological Sciences (PTN) Joint PhD Program, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Chunhui Wang
- Peking University-Tsinghua University-National Institute of Biological Sciences (PTN) Joint PhD Program, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jinyuan Guo
- State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Xiaoqing Jiang
- State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
- Center for Quantitative Biology, Peking University, Beijing, 100871, China
- Institute of Medical Technology, Peking University Health Science Center, Beijing, 100191, China
| | - Jie Tan
- State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Shufang Wu
- State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
- Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | - Peihong Wang
- State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Tingting Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Man Zhou
- State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
- Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | - Zhencheng Fang
- State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
- Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310006, China.
| | - Huaiqiu Zhu
- State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China.
- Center for Quantitative Biology, Peking University, Beijing, 100871, China.
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA.
- Institute of Medical Technology, Peking University Health Science Center, Beijing, 100191, China.
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