51
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Desingu PA, Mishra S, Dindi L, Srinivasan S, Rajmani RS, Ravi V, Tamta AK, Raghu S, Murugasamy K, Pandit AS, Sundaresan NR. PARP1 inhibition protects mice against Japanese encephalitis virus infection. Cell Rep 2023; 42:113103. [PMID: 37676769 DOI: 10.1016/j.celrep.2023.113103] [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] [Received: 06/09/2021] [Revised: 05/20/2023] [Accepted: 08/22/2023] [Indexed: 09/09/2023] Open
Abstract
Japanese encephalitis (JE) is a vector-borne viral disease that causes acute encephalitis in children. Although vaccines have been developed against the JE virus (JEV), no effective antiviral therapy exists. Our study shows that inhibition of poly(ADP-ribose) polymerase 1 (PARP1), an NAD+-dependent (poly-ADP) ribosyl transferase, protects against JEV infection. Interestingly, PARP1 is critical for JEV pathogenesis in Neuro-2a cells and mice. Small molecular inhibitors of PARP1, olaparib, and 3-aminobenzamide (3-AB) significantly reduce clinical signs and viral load in the serum and brains of mice and improve survival. PARP1 inhibition confers protection against JEV infection by inhibiting autophagy. Mechanistically, upon JEV infection, PARP1 PARylates AKT and negatively affects its phosphorylation. In addition, PARP1 transcriptionally upregulates PTEN, the PIP3 phosphatase, negatively regulating AKT. PARP1-mediated AKT inactivation promotes autophagy and JEV pathogenesis by increasing the FoxO activity. Thus, our findings demonstrate PARP1 as a potential mediator of JEV pathogenesis that can be effectively targeted for treating JE.
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Affiliation(s)
- Perumal Arumugam Desingu
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India.
| | - Sneha Mishra
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Lavanya Dindi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Shalini Srinivasan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Raju S Rajmani
- Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru 560012, India
| | - Venkatraman Ravi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Ankit Kumar Tamta
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Sukanya Raghu
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Krishnega Murugasamy
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Anwit Shriniwas Pandit
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Nagalingam R Sundaresan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India.
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52
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Milner DS, Galindo LJ, Irwin NAT, Richards TA. Transporter Proteins as Ecological Assets and Features of Microbial Eukaryotic Pangenomes. Annu Rev Microbiol 2023; 77:45-66. [PMID: 36944262 DOI: 10.1146/annurev-micro-032421-115538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Here we review two connected themes in evolutionary microbiology: (a) the nature of gene repertoire variation within species groups (pangenomes) and (b) the concept of metabolite transporters as accessory proteins capable of providing niche-defining "bolt-on" phenotypes. We discuss the need for improved sampling and understanding of pangenome variation in eukaryotic microbes. We then review the factors that shape the repertoire of accessory genes within pangenomes. As part of this discussion, we outline how gene duplication is a key factor in both eukaryotic pangenome variation and transporter gene family evolution. We go on to outline how, through functional characterization of transporter-encoding genes, in combination with analyses of how transporter genes are gained and lost from accessory genomes, we can reveal much about the niche range, the ecology, and the evolution of virulence of microbes. We advocate for the coordinated systematic study of eukaryotic pangenomes through genome sequencing and the functional analysis of genes found within the accessory gene repertoire.
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Affiliation(s)
- David S Milner
- Department of Biology, University of Oxford, Oxford, United Kingdom;
| | | | - Nicholas A T Irwin
- Department of Biology, University of Oxford, Oxford, United Kingdom;
- Merton College, University of Oxford, Oxford, United Kingdom
| | - Thomas A Richards
- Department of Biology, University of Oxford, Oxford, United Kingdom;
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53
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Melano I, Cheng WC, Kuo LL, Liu YM, Chou YC, Hung MC, Lai MMC, Sher YP, Su WC. A disintegrin and metalloproteinase domain 9 facilitates SARS-CoV-2 entry into cells with low ACE2 expression. Microbiol Spectr 2023; 11:e0385422. [PMID: 37713503 PMCID: PMC10581035 DOI: 10.1128/spectrum.03854-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 07/18/2023] [Indexed: 09/17/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of the Coronavirus disease-19 (COVID-19) pandemic, utilizes angiotensin-converting enzyme 2 (ACE2) as a receptor for virus infection. However, the expression pattern of ACE2 does not coincide with the tissue tropism of SARS-CoV-2, hinting that other host proteins might be involved in facilitating SARS-CoV-2 entry. To explore potential host factors for SARS-CoV-2 entry, we performed an arrayed shRNA screen in H1650 and HEK293T cells. Here, we identified a disintegrin and a metalloproteinase domain 9 (ADAM9) protein as an important host factor for SARS-CoV-2 entry. Our data showed that silencing ADAM9 reduced virus entry, while its overexpression promoted infection. The knockdown of ADAM9 decreased the infectivity of the variants of concern tested-B.1.1.7 (alpha), B.1.617.2 (delta), and B.1.1.529 (omicron). Furthermore, mechanistic studies indicated that ADAM9 is involved in the binding and endocytosis stages of SARS-CoV-2 entry. Through immunoprecipitation experiments, we demonstrated that ADAM9 binds to the S1 subunit of the SARS-CoV-2 Spike. Additionally, ADAM9 can interact with ACE2, and co-expression of both proteins markedly enhances virus infection. Moreover, the enzymatic activity of ADAM9 facilitates virus entry. Our study reveals an insight into the mechanism of SARS-CoV-2 virus entry and elucidates the role of ADAM9 in virus infection. IMPORTANCE COVID-19, an infectious respiratory disease caused by SARS-CoV-2, has greatly impacted global public health and the economy. Extensive vaccination efforts have been launched worldwide over the last couple of years. However, several variants of concern that reduce the efficacy of vaccines have kept emerging. Thereby, further understanding of the mechanism of SARS-CoV-2 entry is indispensable, which will allow the development of an effective antiviral strategy. Here, we identify a disintegrin and metalloproteinase domain 9 (ADAM9) protein as a co-factor of ACE2 important for SARS-CoV-2 entry, even for the variants of concern, and show that ADAM9 interacts with Spike to aid virus entry. This virus-host interaction could be exploited to develop novel therapeutics against COVID-19.
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Affiliation(s)
- Ivonne Melano
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Wei-Chung Cheng
- Ph.D. Program for Cancer Biology and Drug Discovery, China Medical University and Academia Sinica, Taipei, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung, Taiwan
| | - Li-Lan Kuo
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Yuag-Meng Liu
- Department of Internal Medicine, College of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Division of Infectious Diseases, Changhua Christian Medical Foundation, Changhua Christian Hospital, Changhua, Taiwan
| | - Yu Chi Chou
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Mien-Chie Hung
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung, Taiwan
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung, Taiwan
- Center for Molecular Medicine, China Medical University Hospital, Taichung, Taiwan
- Department of Biotechnology, Asia University, Taichung, Taiwan
| | - Michael M. C. Lai
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Yuh-Pyng Sher
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Ph.D. Program for Cancer Biology and Drug Discovery, China Medical University and Academia Sinica, Taipei, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung, Taiwan
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung, Taiwan
- Center for Molecular Medicine, China Medical University Hospital, Taichung, Taiwan
- International Master’s Program of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Wen-Chi Su
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- International Master’s Program of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
- Drug Development Center, China Medical University, Taichung, Taiwan
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54
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Chapman NS, Hulswit RJG, Westover JLB, Stass R, Paesen GC, Binshtein E, Reidy JX, Engdahl TB, Handal LS, Flores A, Gowen BB, Bowden TA, Crowe JE. Multifunctional human monoclonal antibody combination mediates protection against Rift Valley fever virus at low doses. Nat Commun 2023; 14:5650. [PMID: 37704627 PMCID: PMC10499838 DOI: 10.1038/s41467-023-41171-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 08/22/2023] [Indexed: 09/15/2023] Open
Abstract
The zoonotic Rift Valley fever virus (RVFV) can cause severe disease in humans and has pandemic potential, yet no approved vaccine or therapy exists. Here we describe a dual-mechanism human monoclonal antibody (mAb) combination against RVFV that is effective at minimal doses in a lethal mouse model of infection. We structurally analyze and characterize the binding mode of a prototypical potent Gn domain-A-binding antibody that blocks attachment and of an antibody that inhibits infection by abrogating the fusion process as previously determined. Surprisingly, the Gn domain-A antibody does not directly block RVFV Gn interaction with the host receptor low density lipoprotein receptor-related protein 1 (LRP1) as determined by a competitive assay. This study identifies a rationally designed combination of human mAbs deserving of future investigation for use in humans against RVFV infection. Using a two-pronged mechanistic approach, we demonstrate the potent efficacy of a rationally designed combination mAb therapeutic.
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Affiliation(s)
- Nathaniel S Chapman
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Ruben J G Hulswit
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Jonna L B Westover
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, 84322, USA
| | - Robert Stass
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Guido C Paesen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Elad Binshtein
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Joseph X Reidy
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Taylor B Engdahl
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Laura S Handal
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Alejandra Flores
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Brian B Gowen
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, 84322, USA
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - James E Crowe
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
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55
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Si Y, Wu W, Xue X, Sun X, Qin Y, Li Y, Qiu C, Li Y, Zhuo Z, Mi Y, Zheng P. The evolution of SARS-CoV-2 and the COVID-19 pandemic. PeerJ 2023; 11:e15990. [PMID: 37701824 PMCID: PMC10493083 DOI: 10.7717/peerj.15990] [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] [Received: 03/21/2023] [Accepted: 08/08/2023] [Indexed: 09/14/2023] Open
Abstract
Scientists have made great efforts to understand the evolution of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) to provide crucial information to public health experts on strategies to control this viral pathogen. The pandemic of the coronavirus disease that began in 2019, COVID-19, lasted nearly three years, and nearly all countries have set different epidemic prevention policies for this virus. The continuous evolution of SARS-CoV-2 alters its pathogenicity and infectivity in human hosts, thus the policy and treatments have been continually adjusted. Based on our previous study on the dynamics of binding ability prediction between the COVID-19 spike protein and human ACE2, the present study mined over 10 million sequences and epidemiological data of SARS-CoV-2 during 2020-2022 to understand the evolutionary path of SARS-CoV-2. We analyzed and predicted the mutation rates of the whole genome and main proteins of SARS-CoV-2 from different populations to understand the adaptive relationship between humans and COVID-19. Our study identified a correlation of the mutation rates from each protein of SARS-CoV-2 and various human populations. Overall, this analysis provides a scientific basis for developing data-driven strategies to confront human pathogens.
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Affiliation(s)
- Yuanfang Si
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Weidong Wu
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Xia Xue
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Xiangdong Sun
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Yaping Qin
- School of Basic Medical Sciences, Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Ya Li
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Chunjing Qiu
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Yingying Li
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Ziran Zhuo
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yang Mi
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Pengyuan Zheng
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
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56
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Garte S. Targeted Hypermutation as a Survival Strategy: A Theoretical Approach. Acta Biotheor 2023; 71:20. [PMID: 37668864 DOI: 10.1007/s10441-023-09471-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 08/21/2023] [Indexed: 09/06/2023]
Abstract
Targeted hypermutation has proven to be a useful survival strategy for bacteria under severe stress and is also used by multicellular organisms in specific instances such as the mammalian immune system. This might appear surprising, given the generally observed deleterious effects of poor replication fidelity/high mutation rate. A previous theoretical model designed to explore the role of replication fidelity in the origin of life was applied to a simulated hypermutation scenario. The results confirmed that the same model is useful for analyzing hypermutation and can predict the effects of the same parameters (survival probability, replication fidelity, mutation effect, and others) on the survival of cellular populations undergoing hypermutation as a result of severe stress.
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Affiliation(s)
- Seymour Garte
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, 160 Frelinghuysen Road, Piscataway, NJ, 08854-8020, USA.
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57
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Williams EP, Xue Y, Lee J, Fitzpatrick EA, Kong Y, Reichard W, Writt H, Jonsson CB. Deep spatial profiling of Venezuelan equine encephalitis virus reveals increased genetic diversity amidst neuroinflammation and cell death during brain infection. J Virol 2023; 97:e0082723. [PMID: 37560924 PMCID: PMC10506382 DOI: 10.1128/jvi.00827-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 06/20/2023] [Indexed: 08/11/2023] Open
Abstract
Venezuelan equine encephalitis virus (VEEV) causes a febrile illness that can progress to neurological disease with the possibility of death in human cases. The evaluation and optimization of therapeutics that target brain infections demands knowledge of the host's response to VEEV, the dynamics of infection, and the potential for within-host evolution of the virus. We hypothesized that selective pressures during infection of the brain may differ temporally and spatially and so we investigated the dynamics of the host response, viral transcript levels, and genetic variation of VEEV TC-83 in eight areas of the brain in mice over 7 days post-infection (dpi). Viral replication increased throughout the brain until 5-6 dpi and decreased thereafter with neurons as the main site of viral replication. Low levels of genetic diversity were noted on 1 dpi and were followed by an expansion in the genetic diversity of VEEV and nonsynonymous (Ns) mutations that peaked by 5 dpi. The pro-inflammatory response and the influx of immune cells mirrored the levels of virus and correlated with substantial damage to neurons by 5 dpi and increased activation of microglial cells and astrocytes. The prevalence and dynamics of Ns mutations suggest that the VEEV is under selection within the brain and that progressive neuroinflammation may play a role in acting as a selective pressure. IMPORTANCE Treatment of encephalitis in humans caused by Venezuelan equine encephalitis virus (VEEV) from natural or aerosol exposure is not available, and hence, there is a great interest to address this gap. In contrast to natural infections, therapeutic treatment of infections from aerosol exposure will require fast-acting drugs that rapidly penetrate the blood-brain barrier, engage sites of infection in the brain and mitigate the emergence of drug resistance. Therefore, it is important to understand not only VEEV pathogenesis, but the trafficking of the viral population within the brain, the potential for within-host evolution of the virus, and how VEEV might evolve resistance.
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Affiliation(s)
- Evan P. Williams
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Yi Xue
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Jasper Lee
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Elizabeth A. Fitzpatrick
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, Tennessee, USA
- Institute for the Study of Host-Pathogen Systems, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Ying Kong
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Walter Reichard
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Haley Writt
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Colleen B. Jonsson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, Tennessee, USA
- Institute for the Study of Host-Pathogen Systems, University of Tennessee Health Science Center, Memphis, Tennessee, USA
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58
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Roder AE, Johnson KEE, Knoll M, Khalfan M, Wang B, Schultz-Cherry S, Banakis S, Kreitman A, Mederos C, Youn JH, Mercado R, Wang W, Chung M, Ruchnewitz D, Samanovic MI, Mulligan MJ, Lässig M, Luksza M, Das S, Gresham D, Ghedin E. Optimized quantification of intra-host viral diversity in SARS-CoV-2 and influenza virus sequence data. mBio 2023; 14:e0104623. [PMID: 37389439 PMCID: PMC10470513 DOI: 10.1128/mbio.01046-23] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/02/2023] [Indexed: 07/01/2023] Open
Abstract
High error rates of viral RNA-dependent RNA polymerases lead to diverse intra-host viral populations during infection. Errors made during replication that are not strongly deleterious to the virus can lead to the generation of minority variants. However, accurate detection of minority variants in viral sequence data is complicated by errors introduced during sample preparation and data analysis. We used synthetic RNA controls and simulated data to test seven variant-calling tools across a range of allele frequencies and simulated coverages. We show that choice of variant caller and use of replicate sequencing have the most significant impact on single-nucleotide variant (SNV) discovery and demonstrate how both allele frequency and coverage thresholds impact both false discovery and false-negative rates. When replicates are not available, using a combination of multiple callers with more stringent cutoffs is recommended. We use these parameters to find minority variants in sequencing data from SARS-CoV-2 clinical specimens and provide guidance for studies of intra-host viral diversity using either single replicate data or data from technical replicates. Our study provides a framework for rigorous assessment of technical factors that impact SNV identification in viral samples and establishes heuristics that will inform and improve future studies of intra-host variation, viral diversity, and viral evolution. IMPORTANCE When viruses replicate inside a host cell, the virus replication machinery makes mistakes. Over time, these mistakes create mutations that result in a diverse population of viruses inside the host. Mutations that are neither lethal to the virus nor strongly beneficial can lead to minority variants that are minor members of the virus population. However, preparing samples for sequencing can also introduce errors that resemble minority variants, resulting in the inclusion of false-positive data if not filtered correctly. In this study, we aimed to determine the best methods for identification and quantification of these minority variants by testing the performance of seven commonly used variant-calling tools. We used simulated and synthetic data to test their performance against a true set of variants and then used these studies to inform variant identification in data from SARS-CoV-2 clinical specimens. Together, analyses of our data provide extensive guidance for future studies of viral diversity and evolution.
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Affiliation(s)
- A. E. Roder
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
| | - K. E. E. Johnson
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - M. Knoll
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - M. Khalfan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - B. Wang
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - S. Schultz-Cherry
- Department of Infectious Diseases, St Jude Children Research Hospital, Memphis, Tennessee, USA
| | - S. Banakis
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
| | - A. Kreitman
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
| | - C. Mederos
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
| | - J.-H. Youn
- Department of Laboratory Medicine, NIH, Bethesda, Maryland, USA
| | - R. Mercado
- Department of Laboratory Medicine, NIH, Bethesda, Maryland, USA
| | - W. Wang
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
| | - M. Chung
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
| | - D. Ruchnewitz
- Institute for Biological Physics, University of Cologne, Cologne, Germany
| | - M. I. Samanovic
- Department of Medicine, New York University Langone Vaccine Center, New York, New York, USA
| | - M. J. Mulligan
- Department of Medicine, New York University Langone Vaccine Center, New York, New York, USA
| | - M. Lässig
- Institute for Biological Physics, University of Cologne, Cologne, Germany
| | - M. Luksza
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - S. Das
- Department of Laboratory Medicine, NIH, Bethesda, Maryland, USA
| | - D. Gresham
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - E. Ghedin
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
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Aguilar Rangel M, Dolan PT, Taguwa S, Xiao Y, Andino R, Frydman J. High-resolution mapping reveals the mechanism and contribution of genome insertions and deletions to RNA virus evolution. Proc Natl Acad Sci U S A 2023; 120:e2304667120. [PMID: 37487061 PMCID: PMC10400975 DOI: 10.1073/pnas.2304667120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/07/2023] [Indexed: 07/26/2023] Open
Abstract
RNA viruses rapidly adapt to selective conditions due to the high intrinsic mutation rates of their RNA-dependent RNA polymerases (RdRps). Insertions and deletions (indels) in viral genomes are major contributors to both deleterious mutational load and evolutionary novelty, but remain understudied. To characterize the mechanistic details of their formation and evolutionary dynamics during infection, we developed a hybrid experimental-bioinformatic approach. This approach, called MultiMatch, extracts insertions and deletions from ultradeep sequencing experiments, including those occurring at extremely low frequencies, allowing us to map their genomic distribution and quantify the rates at which they occur. Mapping indel mutations in adapting poliovirus and dengue virus populations, we determine the rates of indel generation and identify mechanistic and functional constraints shaping indel diversity. Using poliovirus RdRp variants of distinct fidelity and genome recombination rates, we demonstrate tradeoffs between fidelity and Indel generation. Additionally, we show that maintaining translation frame and viral RNA structures constrain the Indel landscape and that, due to these significant fitness effects, Indels exert a significant deleterious load on adapting viral populations. Conversely, we uncover positively selected Indels that modulate RNA structure, generate protein variants, and produce defective interfering genomes in viral populations. Together, our analyses establish the kinetic and mechanistic tradeoffs between misincorporation, recombination, and Indel rates and reveal functional principles defining the central role of Indels in virus evolution, emergence, and the regulation of viral infection.
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Affiliation(s)
| | - Patrick T. Dolan
- Department of Biology, Stanford University, Stanford, CA94305
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA94143
| | - Shuhei Taguwa
- Department of Biology, Stanford University, Stanford, CA94305
- Research Institute for Microbial Diseases, Osaka University, Yamadaoka, Suita, Osaka565-0871, Japan
| | - Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA94143
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA94143
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA94305
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Kane Y, Chen J, Li L, Descorps-Declère S, Wong G, Berthet N. Diverse single-stranded DNA viruses from viral metagenomics on a cynopterus bat in China. Heliyon 2023; 9:e18270. [PMID: 37520955 PMCID: PMC10374907 DOI: 10.1016/j.heliyon.2023.e18270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 08/01/2023] Open
Abstract
Bats serve as reservoirs for many emerging viruses. Cressdnaviruses can infect a wide range of animals, including agricultural species, such as pigs, in which porcine circoviruses cause severe gastroenteritis. New cressdnaviruses have also attracted considerable attention recently, due to their involvement with infectious diseases. However, little is known about their host range and many cressdnaviruses remain poorly characterized. We identified and characterized 11 contigs consisting of previously unknown cressdnaviruses from a rectal swab sample of a Cynopterus bat collected in Yunnan Province, China, in 2011. Full genomes of two cressdnaviruses (OQ267680, 2069 nt; OQ351951, 2382 nt), and a nearly complete genome for a third (OQ267683, 2361 nt) were obtained. Phylogenetic analyses and the characteristics of these viral genomes suggest a high degree of ssDNA virus diversity. These results shed light on cressdnavirus diversity and the probable role of Cynopterus bats as their hosts.
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Affiliation(s)
- Yakhouba Kane
- Viral Hemorrhagic Fevers Research Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Linmiao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Stéphane Descorps-Declère
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Gary Wong
- Viral Hemorrhagic Fevers Research Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Nicolas Berthet
- Centre for Microbes, Development and Health, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Discovery and Molecular Characterization of Pathogens Unit, Shanghai 200031, China
- Institut Pasteur, Unité Environnement et Risque Infectieux, Cellule D’Intervention Biologique D’Urgence, 75015 Paris, France
- Institut Pasteur, Université Paris-Cité, Unité Epidémiologie et Physiopathologie des Virus Oncogènes, 75724 Paris, France
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61
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Kim IJ, Lee YH, Khalid MM, Chen IP, Zhang Y, Ott M, Verdin E. SARS-CoV-2 protein ORF8 limits expression levels of Spike antigen and facilitates immune evasion of infected host cells. J Biol Chem 2023; 299:104955. [PMID: 37354973 PMCID: PMC10289268 DOI: 10.1016/j.jbc.2023.104955] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/26/2023] Open
Abstract
Recovery from COVID-19 depends on the ability of the host to effectively neutralize virions and infected cells, a process largely driven by antibody-mediated immunity. However, with the newly emerging variants that evade Spike-targeting antibodies, re-infections and breakthrough infections are increasingly common. A full characterization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mechanisms counteracting antibody-mediated immunity is therefore needed. Here, we report that ORF8 is a virally encoded SARS-CoV-2 factor that controls cellular Spike antigen levels. We show that ORF8 limits the availability of mature Spike by inhibiting host protein synthesis and retaining Spike at the endoplasmic reticulum, reducing cell-surface Spike levels and recognition by anti-SARS-CoV-2 antibodies. In conditions of limited Spike availability, we found ORF8 restricts Spike incorporation during viral assembly, reducing Spike levels in virions. Cell entry of these virions then leaves fewer Spike molecules at the cell surface, limiting antibody recognition of infected cells. Based on these findings, we propose that SARS-CoV-2 variants may adopt an ORF8-dependent strategy that facilitates immune evasion of infected cells for extended viral production.
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Affiliation(s)
- Ik-Jung Kim
- Buck Institute for Research on Aging, Novato, California, United States.
| | - Yong-Ho Lee
- Buck Institute for Research on Aging, Novato, California, United States; Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Mir M Khalid
- Gladstone Institutes, San Francisco, California, United States; Department of Medicine, University of California, San Francisco, San Francisco, California, United States
| | - Irene P Chen
- Gladstone Institutes, San Francisco, California, United States; Department of Medicine, University of California, San Francisco, San Francisco, California, United States
| | - Yini Zhang
- Buck Institute for Research on Aging, Novato, California, United States
| | - Melanie Ott
- Gladstone Institutes, San Francisco, California, United States; Department of Medicine, University of California, San Francisco, San Francisco, California, United States; Chan Zuckerberg Biohub, San Francisco, California, United States
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, California, United States.
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Ramakrishnan J, Chinnamadhu A, Suresh S, Poomani K. Probing the binding nature and stability of highly transmissible mutated variant alpha to omicron of SARS-CoV-2 RBD with ACE2 via molecular dynamics simulation. J Cell Biochem 2023; 124:1115-1134. [PMID: 37435893 DOI: 10.1002/jcb.30432] [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] [Received: 02/03/2023] [Revised: 05/20/2023] [Accepted: 05/23/2023] [Indexed: 07/13/2023]
Abstract
Currently, no approved drug is available as a causative agent of coronavirus disease 2019 (COVID-19) except for some repurposed drugs. The first structure of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in late 2019, based on that some vaccines and repurposed drugs were approved to prevent people from COVID-19 during the pandemic situation. Since then, new types of variants emerged and notably, the receptor binding domain (RBD) adopted different binding modes with angiotensin-converting enzyme 2 (ACE2); this made significant changes in the progression of COVID-19. Some of the new variants are highly infectious spreading fast and dangerous. The present study is focused on understanding the binding mode of the RBD of different mutated SARS-CoV-2 variants of concern (alpha to omicron) with the human ACE2 using molecular dynamics simulation. Notably, some variants adopted a new binding mode of RBD with ACE2 and formed different interactions, which is unlike the wild type; this was confirmed from the comparison of interaction between RBD-ACE2 of all variants with its wild-type structure. Binding energy values confirm that some mutated variants exhibit high binding affinity. These findings demonstrate that the variations in the sequence of SARS-CoV-2 S-protein altered the binding mode of RBD; this may be the reason that the virus has high transmissibility and causes new infections. This in-silico study on mutated variants of SARS-CoV-2 RBD with ACE2 insights into their binding mode, binding affinity, and stability. This information may help to understand the RBD-ACE2 binding domains, which allows for designing newer drugs and vaccines.
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Affiliation(s)
- Jaganathan Ramakrishnan
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Archana Chinnamadhu
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Suganya Suresh
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Kumaradhas Poomani
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
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Biancolella M, Colona VL, Luzzatto L, Watt JL, Mattiuz G, Conticello SG, Kaminski N, Mehrian-Shai R, Ko AI, Gonsalves GS, Vasiliou V, Novelli G, Reichardt JKV. COVID-19 annual update: a narrative review. Hum Genomics 2023; 17:68. [PMID: 37488607 PMCID: PMC10367267 DOI: 10.1186/s40246-023-00515-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/16/2023] [Indexed: 07/26/2023] Open
Abstract
Three and a half years after the pandemic outbreak, now that WHO has formally declared that the emergency is over, COVID-19 is still a significant global issue. Here, we focus on recent developments in genetic and genomic research on COVID-19, and we give an outlook on state-of-the-art therapeutical approaches, as the pandemic is gradually transitioning to an endemic situation. The sequencing and characterization of rare alleles in different populations has made it possible to identify numerous genes that affect either susceptibility to COVID-19 or the severity of the disease. These findings provide a beginning to new avenues and pan-ethnic therapeutic approaches, as well as to potential genetic screening protocols. The causative virus, SARS-CoV-2, is still in the spotlight, but novel threatening virus could appear anywhere at any time. Therefore, continued vigilance and further research is warranted. We also note emphatically that to prevent future pandemics and other world-wide health crises, it is imperative to capitalize on what we have learnt from COVID-19: specifically, regarding its origins, the world's response, and insufficient preparedness. This requires unprecedented international collaboration and timely data sharing for the coordination of effective response and the rapid implementation of containment measures.
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Affiliation(s)
| | - Vito Luigi Colona
- Department of Biomedicine and Prevention, School of Medicine and Surgery, Tor Vergata University of Rome, Via Montpellier 1, 00133, Rome, Italy
| | - Lucio Luzzatto
- Department of Haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- University of Florence, 50121, Florence, Italy
| | - Jessica Lee Watt
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Smithfield, QLD, 4878, Australia
| | | | - Silvestro G Conticello
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Florence, Italy
- Institute of Clinical Physiology - National Council of Research (IFC-CNR), 56124, Pisa, Italy
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Ruty Mehrian-Shai
- Pediatric Hemato-Oncology, Edmond and Lilly Safra Children's Hospital, Sheba Medical Center, Tel Hashomer 2 Sheba Road, 52621, Ramat Gan, Israel
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, USA
- Instituto Gonçalo MonizFundação Oswaldo Cruz, Salvador, Bahia, Brazil
| | - Gregg S Gonsalves
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, USA
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, School of Medicine and Surgery, Tor Vergata University of Rome, Via Montpellier 1, 00133, Rome, Italy.
- IRCCS Neuromed, 86077, Pozzilli, IS, Italy.
- Department of Pharmacology, School of Medicine, University of Nevada, 89557, Reno, NV, USA.
| | - Juergen K V Reichardt
- Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield, QLD, 4878, Australia
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64
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Bondaryuk AN, Belykh OI, Andaev EI, Bukin YS. Inferring Evolutionary Timescale of Omsk Hemorrhagic Fever Virus. Viruses 2023; 15:1576. [PMID: 37515262 PMCID: PMC10385366 DOI: 10.3390/v15071576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Until 2020, there were only three original complete genome (CG) nucleotide sequences of Omsk hemorrhagic fever virus (OHFV) in GenBank. For this reason, the evolutionary rate and divergence time assessments reported in the literature were based on the E gene sequences, but notably without temporal signal evaluation, such that their reliability is unclear. As of July 2022, 47 OHFV CG sequences have been published, which enables testing of temporal signal in the data and inferring unbiased and reliable substitution rate and divergence time values. Regression analysis in the TempEst software demonstrated a stronger clocklike behavior in OHFV samples for the complete open reading frame (ORF) data set (R2 = 0.42) than for the E gene data set (R2 = 0.11). Bayesian evaluation of temporal signal indicated very strong evidence, with a log Bayes factor of more than 5, in favor of temporal signal in all data sets. Our results based on the complete ORF sequences showed a more precise OHFV substitution rate (95% highest posterior density (HPD) interval, 9.1 × 10-5-1.8 × 10-4 substitutions per site per year) and tree root height (416-896 years ago) compared with previous assessments. The rate obtained is significantly higher than tick-borne encephalitis virus by at least 3.8-fold. The phylogenetic analysis and past population dynamics reconstruction revealed the declining trend of OHFV genetic diversity, but there was phylogenomic evidence that implicit virus subpopulations evolved locally and underwent an exponential growth phase.
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Affiliation(s)
- Artem N Bondaryuk
- Laboratory of Natural Focal Viral Infections, Irkutsk Antiplague Research Institute of Siberia and the Far East, Irkutsk 664047, Russia
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk 664033, Russia
| | - Olga I Belykh
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk 664033, Russia
| | - Evgeny I Andaev
- Laboratory of Natural Focal Viral Infections, Irkutsk Antiplague Research Institute of Siberia and the Far East, Irkutsk 664047, Russia
| | - Yurij S Bukin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk 664033, Russia
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65
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Chen HC. A systematic review of the barcoding strategy that contributes to COVID-19 diagnostics at a population level. Front Mol Biosci 2023; 10:1141534. [PMID: 37496777 PMCID: PMC10366608 DOI: 10.3389/fmolb.2023.1141534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 06/30/2023] [Indexed: 07/28/2023] Open
Abstract
The outbreak of SARS-CoV-2 has made us more alert to the importance of viral diagnostics at a population level to rapidly control the spread of the disease. The critical question would be how to scale up testing capacity and perform a diagnostic test in a high-throughput manner with robust results and affordable costs. Here, the latest 26 articles using barcoding technology for COVID-19 diagnostics and biologically-relevant studies are reviewed. Barcodes are molecular tags, that allow proceeding an array of samples at once. To date, barcoding technology followed by high-throughput sequencing has been made for molecular diagnostics for SARS-CoV-2 infections because it can synchronously analyze up to tens of thousands of clinical samples within a short diagnostic time. Essentially, this technology can also be used together with different biotechnologies, allowing for investigation with resolution of single molecules. In this Mini-Review, I first explain the general principle of the barcoding strategy and then put forward recent studies using this technology to accomplish COVID-19 diagnostics and basic research. In the meantime, I provide the viewpoint to improve the current COVID-19 diagnostic strategy with potential solutions. Finally, and importantly, two practical ideas about how barcodes can be further applied in studying SARS-CoV-2 to accelerate our understanding of this virus are proposed.
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66
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Chetta M, Cammarota AL, De Marco M, Bukvic N, Marzullo L, Rosati A. The Continuous Adaptive Challenge Played by Arboviruses: An In Silico Approach to Identify a Possible Interplay between Conserved Viral RNA Sequences and Host RNA Binding Proteins (RBPs). Int J Mol Sci 2023; 24:11051. [PMID: 37446229 DOI: 10.3390/ijms241311051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/20/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Climate change and globalization have raised the risk of vector-borne disease (VBD) introduction and spread in various European nations in recent years. In Italy, viruses carried by tropical vectors have been shown to cause viral encephalitis, one of the symptoms of arboviruses, a spectrum of viral disorders spread by arthropods such as mosquitoes and ticks. Arboviruses are currently causing alarm and attention, and the World Health Organization (WHO) has released recommendations to adopt essential measures, particularly during the hot season, to restrict the spreading of the infectious agents among breeding stocks. In this scenario, rapid analysis systems are required, because they can quickly provide information on potential virus-host interactions, the evolution of the infection, and the onset of disabling clinical symptoms, or serious illnesses. Such systems include bioinformatics approaches integrated with molecular evaluation. Viruses have co-evolved different strategies to transcribe their own genetic material, by changing the host's transcriptional machinery, even in short periods of time. The introduction of genetic alterations, particularly in RNA viruses, results in a continuous adaptive fight against the host's immune system. We propose an in silico pipeline method for performing a comprehensive motif analysis (including motif discovery) on entire genome sequences to uncover viral sequences that may interact with host RNA binding proteins (RBPs) by interrogating the database of known RNA binding proteins, which play important roles in RNA metabolism and biological processes. Indeed, viral RNA sequences, able to bind host RBPs, may compete with cellular RNAs, altering important metabolic processes. Our findings suggest that the proposed in silico approach could be a useful and promising tool to investigate the complex and multiform clinical manifestations of viral encephalitis, and possibly identify altered metabolic pathways as targets of pharmacological treatments and innovative therapeutic protocols.
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Affiliation(s)
- Massimiliano Chetta
- U.O.C. Medical and Laboratory Genetics, A.O.R.N., Cardarelli, 80131 Naples, Italy
| | - Anna Lisa Cammarota
- Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, 84084 Baronissi, SA, Italy
| | - Margot De Marco
- Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, 84084 Baronissi, SA, Italy
- FIBROSYS s.r.l. Academic Spin-Off, University of Salerno, 84084 Baronissi, Italy
| | - Nenad Bukvic
- Medical Genetics Section, University Hospital Consortium Corporation Polyclinics of Bari, 70124 Bari, Italy
| | - Liberato Marzullo
- Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, 84084 Baronissi, SA, Italy
- FIBROSYS s.r.l. Academic Spin-Off, University of Salerno, 84084 Baronissi, Italy
| | - Alessandra Rosati
- Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, 84084 Baronissi, SA, Italy
- FIBROSYS s.r.l. Academic Spin-Off, University of Salerno, 84084 Baronissi, Italy
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Brown OR, Hullender DA. Biological evolution requires an emergent, self-organizing principle. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023:S0079-6107(23)00058-5. [PMID: 37343790 DOI: 10.1016/j.pbiomolbio.2023.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/16/2023] [Accepted: 06/09/2023] [Indexed: 06/23/2023]
Abstract
In this perspective review, we assess fundamental flaws in Darwinian evolution, including its modern versions. Fixed mutations 'explain' microevolution but not macroevolution including speciation events and the origination of all the major body plans of the Cambrian explosion. Complex, multifactorial change is required for speciation events and inevitably requires self-organization beyond what is accomplished by known mechanisms. The assembly of ribosomes and ATP synthase are specific examples. We propose their origin is a model for what is unexplained in biological evolution. Probability of evolution is modeled in Section 9 and values are absurdly improbable. Speciation and higher taxonomic changes become exponentially less probable as the number of required, genetically-based events increase. Also, the power required of the proposed selection mechanism (survival of the fittest) is nil for any biological advance requiring multiple changes, because they regularly occur in multiple generations (different genomes) and would not be selectively conserved by the concept survival of the fittest (a concept ultimately centered on the individual). Thus, survival of the fittest cannot 'explain' the origin of the millions of current and extinct species. We also focus on the inadequacies of laboratory chemistry to explain the complex, required biological self-organization seen in cells. We propose that a 'bioelectromagnetic' field/principle emerges in living cells. Synthesis by self-organization of massive molecular complexes involves biochemical responses to this emergent field/principle. There are ramifications for philosophy, science, and religion. Physics and mathematics must be more strongly integrated with biology and integration should receive dedicated funding with special emphasis for medical applications; treatment of cancer and genetic diseases are examples.
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Affiliation(s)
- Olen R Brown
- Emeritus of Biomedical Sciences, at the University of Missouri, Columbia, MO, USA.
| | - David A Hullender
- Mechanical and Aerospace Engineering at the University of Texas at Arlington, USA
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Choi YM, Kim DH, Jang J, Kim BJ. A hepatitis B virus-derived peptide combined with HBsAg exerts an anti-HBV effect in an HBV transgenic mouse model as a therapeutic vaccine. Front Immunol 2023; 14:1155637. [PMID: 37334373 PMCID: PMC10272379 DOI: 10.3389/fimmu.2023.1155637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/18/2023] [Indexed: 06/20/2023] Open
Abstract
Introduction For complete or functional cure of hepatitis B virus (HBV) infection, application of immunotherapy is now being attempted. Recently, we reported that a 6-mer hepatitis B virus (HBV)-derived peptide, Poly6, exerts a strong anticancer effect in tumor-implanted mice through inducible nitric oxide synthase (iNOS)-producing DCs (Tip-DCs) in a type 1 interferon (IFN-I)-dependent manner, suggesting its potential as a vaccine adjuvant. Methods In this study, we explored the potential of Poly6 in combination with HBsAg as a therapeutic vaccine against hepatitis B virus infection. We investigated the immunotherapeutic potential of Poly6 combined with HBsAg vaccination against hepatitis B virus infection in C57BL/6 mice or an HBV transgenic mouse model. Results In C57BL/6 mice, Poly6 enhanced DC maturation and DC migration capacity in an IFN-I-dependent manner. Moreover, the addition of Poly6 to alum in combination with HBsAg also led to enhanced HBsAg-specific cell-mediated immune (CMI) responses, suggesting its potential as an adjuvant of HBsAg-based vaccines. In HBV transgenic mice, vaccination with Poly6 combined with HBsAg exerted a strong anti-HBV effect via induction of HBV-specific humoral and cell-mediated immune responses. In addition, it also induced HBV-specific effector memory T cells (TEM). Discussion Our data indicated that vaccination with Poly6 in combination with HBsAg exerts an anti-HBV effect in HBV transgenic mice, which is mainly mediated by HBV-specific CMI and humoral immune responses via IFN-I-dependent DC activation, suggesting the feasibility of Poly6 as an adjuvant for an HBV therapeutic vaccine.
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Affiliation(s)
- Yu-Min Choi
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Dong Hyun Kim
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Junghwa Jang
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Bum-Joon Kim
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Liver Research Institute, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cancer Research Institute, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Department of Microbiology and Immunology, Seoul National University Medical Research Center (SNUMRC), Seoul, Republic of Korea
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Zeghbib S, Kemenesi G, Jakab F. The importance of equally accessible genomic surveillance in the age of pandemics. Biol Futur 2023; 74:81-89. [PMID: 37199870 PMCID: PMC10193332 DOI: 10.1007/s42977-023-00164-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 03/29/2023] [Indexed: 05/19/2023]
Abstract
Genomic epidemiology is now a core component in investigating the spread of a disease during an outbreak and for future preparedness to tackle emerging zoonoses. During the last decades, several viral diseases arose and emphasized the importance of molecular epidemiology in tracking the dispersal route, supporting proper mitigation measures, and appropriate vaccine development. In this perspective article, we summarized what has been done so far in the genomic epidemiology field and what should be considered in the future. We traced back the methods and protocols employed over time for zoonotic disease response. Either to small outbreaks such as the severe acute respiratory syndrome (SARS) outbreak identified first in 2002 in Guangdong, China, or to a global pandemic like the one that we are experiencing now since 2019 when the severe acute respiratory syndrome 2 (SARS-CoV-2) virus emerged in Wuhan, China, following several pneumonia cases, and subsequently spread worldwide. We explored both the benefits and shortages encountered when relying on genomic epidemiology, and we clearly present the disadvantages of inequity in accessing these tools around the world, especially in countries with less developed economies. For effectively addressing future pandemics, it is crucial to work for better sequencing equity around the globe.
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Affiliation(s)
- Safia Zeghbib
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pecs, Hungary.
| | - Gábor Kemenesi
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pecs, Hungary
- Faculty of Sciences, Institute of Biology, University of Pécs, Pecs, Hungary
| | - Ferenc Jakab
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pecs, Hungary
- Faculty of Sciences, Institute of Biology, University of Pécs, Pecs, Hungary
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Nicoletto G, Richter SN, Frasson I. Presence, Location and Conservation of Putative G-Quadruplex Forming Sequences in Arboviruses Infecting Humans. Int J Mol Sci 2023; 24:ijms24119523. [PMID: 37298474 DOI: 10.3390/ijms24119523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/12/2023] [Accepted: 05/12/2023] [Indexed: 06/12/2023] Open
Abstract
Guanine quadruplexes (G4s) are non-canonical nucleic acid structures formed by guanine (G)-rich tracts that assemble into a core of stacked planar tetrads. G4s are found in the human genome and in the genomes of human pathogens, where they are involved in the regulation of gene expression and genome replication. G4s have been proposed as novel pharmacological targets in humans and their exploitation for antiviral therapy is an emerging research topic. Here, we report on the presence, conservation and localization of putative G4-forming sequences (PQSs) in human arboviruses. The prediction of PQSs was performed on more than twelve thousand viral genomes, belonging to forty different arboviruses that infect humans, and revealed that the abundance of PQSs in arboviruses is not related to the genomic GC content, but depends on the type of nucleic acid that constitutes the viral genome. Positive-strand ssRNA arboviruses, especially Flaviviruses, are significantly enriched in highly conserved PQSs, located in coding sequences (CDSs) or untranslated regions (UTRs). In contrast, negative-strand ssRNA and dsRNA arboviruses contain few conserved PQSs. Our analyses also revealed the presence of bulged PQSs, accounting for 17-26% of the total predicted PQSs. The data presented highlight the presence of highly conserved PQS in human arboviruses and present non-canonical nucleic acid-structures as promising therapeutic targets in arbovirus infections.
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Affiliation(s)
- Giulia Nicoletto
- Department of Molecular Medicine, University of Padua, Via A. Gabelli 63, 35121 Padua, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, Via A. Gabelli 63, 35121 Padua, Italy
| | - Ilaria Frasson
- Department of Molecular Medicine, University of Padua, Via A. Gabelli 63, 35121 Padua, Italy
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71
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Caspi I, Meir M, Ben Nun N, Abu Rass R, Yakhini U, Stern A, Ram Y. Mutation rate, selection, and epistasis inferred from RNA virus haplotypes via neural posterior estimation. Virus Evol 2023; 9:vead033. [PMID: 37305706 PMCID: PMC10256221 DOI: 10.1093/ve/vead033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/30/2023] [Accepted: 05/16/2023] [Indexed: 06/13/2023] Open
Abstract
RNA viruses are particularly notorious for their high levels of genetic diversity, which is generated through the forces of mutation and natural selection. However, disentangling these two forces is a considerable challenge, and this may lead to widely divergent estimates of viral mutation rates, as well as difficulties in inferring the fitness effects of mutations. Here, we develop, test, and apply an approach aimed at inferring the mutation rate and key parameters that govern natural selection, from haplotype sequences covering full-length genomes of an evolving virus population. Our approach employs neural posterior estimation, a computational technique that applies simulation-based inference with neural networks to jointly infer multiple model parameters. We first tested our approach on synthetic data simulated using different mutation rates and selection parameters while accounting for sequencing errors. Reassuringly, the inferred parameter estimates were accurate and unbiased. We then applied our approach to haplotype sequencing data from a serial passaging experiment with the MS2 bacteriophage, a virus that parasites Escherichia coli. We estimated that the mutation rate of this phage is around 0.2 mutations per genome per replication cycle (95% highest density interval: 0.051-0.56). We validated this finding with two different approaches based on single-locus models that gave similar estimates but with much broader posterior distributions. Furthermore, we found evidence for reciprocal sign epistasis between four strongly beneficial mutations that all reside in an RNA stem loop that controls the expression of the viral lysis protein, responsible for lysing host cells and viral egress. We surmise that there is a fine balance between over- and underexpression of lysis that leads to this pattern of epistasis. To recap, we have developed an approach for joint inference of the mutation rate and selection parameters from full haplotype data with sequencing errors and used it to reveal features governing MS2 evolution.
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Affiliation(s)
- Itamar Caspi
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel
| | - Moran Meir
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel
| | - Nadav Ben Nun
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel
| | | | - Uri Yakhini
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel
| | | | - Yoav Ram
- *Corresponding author: E-mail: ;
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72
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Castrodeza-Sanz J, Sanz-Muñoz I, Eiros JM. Adjuvants for COVID-19 Vaccines. Vaccines (Basel) 2023; 11:vaccines11050902. [PMID: 37243006 DOI: 10.3390/vaccines11050902] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/25/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
In recent decades, the improvement of traditional vaccines has meant that we have moved from inactivated whole virus vaccines, which provoke a moderate immune response but notable adverse effects, to much more processed vaccines such as protein subunit vaccines, which despite being less immunogenic have better tolerability profiles. This reduction in immunogenicity is detrimental to the prevention of people at risk. For this reason, adjuvants are a good solution to improve the immunogenicity of this type of vaccine, with much better tolerability profiles and a low prevalence of side effects. During the COVID-19 pandemic, vaccination focused on mRNA-type and viral vector vaccines. However, during the years 2022 and 2023, the first protein-based vaccines began to be approved. Adjuvanted vaccines are capable of inducing potent responses, not only humoral but also cellular, in populations whose immune systems are weak or do not respond properly, such as the elderly. Therefore, this type of vaccine should complete the portfolio of existing vaccines, and could help to complete vaccination against COVID-19 worldwide now and over the coming years. In this review we analyze the advantages and disadvantages of adjuvants, as well as their use in current and future vaccines against COVID-19.
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Affiliation(s)
- Javier Castrodeza-Sanz
- National Influenza Centre, 47005 Valladolid, Spain
- Preventive Medicine and Public Health Unit, Hospital Clínico Universitario de Valladolid, 47003 Valladolid, Spain
| | - Iván Sanz-Muñoz
- National Influenza Centre, 47005 Valladolid, Spain
- Instituto de Estudios de Ciencias de la Salud de Castilla y León, ICSCYL, 42002 Soria, Spain
| | - Jose M Eiros
- National Influenza Centre, 47005 Valladolid, Spain
- Microbiology Unit, Hospital Clínico Universitario de Valladolid, 47003 Valladolid, Spain
- Microbiology Unit, Hospital Universitario Río Hortega, 47013 Valladolid, Spain
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73
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Bloom JD, Beichman AC, Neher RA, Harris K. Evolution of the SARS-CoV-2 Mutational Spectrum. Mol Biol Evol 2023; 40:msad085. [PMID: 37039557 PMCID: PMC10124870 DOI: 10.1093/molbev/msad085] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/07/2023] [Accepted: 04/06/2023] [Indexed: 04/12/2023] Open
Abstract
SARS-CoV-2 evolves rapidly in part because of its high mutation rate. Here, we examine whether this mutational process itself has changed during viral evolution. To do this, we quantify the relative rates of different types of single-nucleotide mutations at 4-fold degenerate sites in the viral genome across millions of human SARS-CoV-2 sequences. We find clear shifts in the relative rates of several types of mutations during SARS-CoV-2 evolution. The most striking trend is a roughly 2-fold decrease in the relative rate of G→T mutations in Omicron versus early clades, as was recently noted by Ruis et al. (2022. Mutational spectra distinguish SARS-CoV-2 replication niches. bioRxiv, doi:10.1101/2022.09.27.509649). There is also a decrease in the relative rate of C→T mutations in Delta, and other subtle changes in the mutation spectrum along the phylogeny. We speculate that these changes in the mutation spectrum could arise from viral mutations that affect genome replication, packaging, and antagonization of host innate-immune factors, although environmental factors could also play a role. Interestingly, the mutation spectrum of Omicron is more similar than that of earlier SARS-CoV-2 clades to the spectrum that shaped the long-term evolution of sarbecoviruses. Overall, our work shows that the mutation process is itself a dynamic variable during SARS-CoV-2 evolution and suggests that human SARS-CoV-2 may be trending toward a mutation spectrum more similar to that of other animal sarbecoviruses.
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Affiliation(s)
- Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA
- Department of Genome Sciences, University of Washington, Seattle, WA
- Howard Hughes Medical Institute, Seattle, WA
| | | | - Richard A Neher
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kelley Harris
- Department of Genome Sciences, University of Washington, Seattle, WA
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74
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Veith T, Bleicker T, Eschbach-Bludau M, Brünink S, Mühlemann B, Schneider J, Beheim-Schwarzbach J, Rakotondranary SJ, Ratovonamana YR, Tsagnangara C, Ernest R, Randriantafika F, Sommer S, Stetter N, Jones TC, Drosten C, Ganzhorn JU, Corman VM. Non-structural genes of novel lemur adenoviruses reveal codivergence of virus and host. Virus Evol 2023; 9:vead024. [PMID: 37091898 PMCID: PMC10121206 DOI: 10.1093/ve/vead024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 03/06/2023] [Accepted: 03/27/2023] [Indexed: 03/29/2023] Open
Abstract
Adenoviruses (AdVs) are important human and animal pathogens and are frequently used as vectors for gene therapy and vaccine delivery. Surprisingly, there are only scant data regarding primate AdV origin and evolution, especially in the most basal primate hosts. We detect and sequence AdVs from faeces of two Madagascan lemur species. Complete genome sequence analyses define a new AdV species with a particularly large gene encoding a protein of unknown function in the early gene region 3. Unexpectedly, the new AdV species is not most similar to human or other simian AdVs but to bat adenovirus C. Genome characterisation shows signals of virus-host codivergence in non-structural genes, which show lower diversity than structural genes. Outside a lemur species mixing zone, recombination less frequently separates structural genes, as in human adenovirus C. The evolutionary history of lemur AdVs likely involves both a host switch and codivergence with the lemur hosts.
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Affiliation(s)
- Talitha Veith
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
| | - Tobias Bleicker
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
| | - Monika Eschbach-Bludau
- Institute of Virology, University Hospital, University of Bonn, Venusberg-Campus 1, Bonn 53127, Germany
| | - Sebastian Brünink
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
| | - Barbara Mühlemann
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
- German Centre for Infection Research (DZIF), Partner Site Berlin, Charitéplatz 1, Berlin 10117, Germany
| | - Julia Schneider
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
- German Centre for Infection Research (DZIF), Partner Site Berlin, Charitéplatz 1, Berlin 10117, Germany
| | - Jörn Beheim-Schwarzbach
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
| | - S Jacques Rakotondranary
- Institute of Cell and Systems Biology of Animals, Universität Hamburg, Martin-Luther-King Platz 3, Hamburg 20146, Germany
- Département Biologie Animale, Faculté des Sciences, Université d’ Antananarivo, P.O. Box 906, Antananarivo 101, Madagascar
| | - Yedidya R Ratovonamana
- Institute of Cell and Systems Biology of Animals, Universität Hamburg, Martin-Luther-King Platz 3, Hamburg 20146, Germany
- Département Biologie Animale, Faculté des Sciences, Université d’ Antananarivo, P.O. Box 906, Antananarivo 101, Madagascar
| | - Cedric Tsagnangara
- Tropical Biodiversity and Social Enterprise SARL, Immeuble CNAPS, premier étage, Fort Dauphin 614, Madagascar
| | - Refaly Ernest
- Tropical Biodiversity and Social Enterprise SARL, Immeuble CNAPS, premier étage, Fort Dauphin 614, Madagascar
| | | | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein Allee 11, Ulm 89069, Germany
| | - Nadine Stetter
- Institute of Cell and Systems Biology of Animals, Universität Hamburg, Martin-Luther-King Platz 3, Hamburg 20146, Germany
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, Hamburg 20359, Germany
| | - Terry C Jones
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
- German Centre for Infection Research (DZIF), Partner Site Berlin, Charitéplatz 1, Berlin 10117, Germany
| | - Jörg U Ganzhorn
- Institute of Cell and Systems Biology of Animals, Universität Hamburg, Martin-Luther-King Platz 3, Hamburg 20146, Germany
| | - Victor M Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
- German Centre for Infection Research (DZIF), Partner Site Berlin, Charitéplatz 1, Berlin 10117, Germany
- Labor Berlin, Charité—Vivantes GmbH, Sylter Straße 2, Berlin 13353, Germany
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75
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Kim K, Choi YM, Kim DH, Jang J, Choe WH, Kim BJ. Locked nucleic acid real-time polymerase chain reaction method identifying two polymorphisms of hepatitis B virus genotype C2 infections, rt269L and rt269I. World J Gastroenterol 2023; 29:1721-1734. [PMID: 37077521 PMCID: PMC10107212 DOI: 10.3748/wjg.v29.i11.1721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/13/2023] [Accepted: 02/27/2023] [Indexed: 03/17/2023] Open
Abstract
BACKGROUND The presence of two distinct hepatitis B virus (HBV) Pol RT polymorphisms, rt269L and rt269I, could contribute to the unique clinical or virological phenotype of HBV genotype C2. Therefore, a simple and sensitive method capable of identifying both types in chronic hepatitis B (CHB) patients infected with genotype C2 should be developed.
AIM To develop a novel simple and sensitive locked nucleic acid (LNA)-real time-polymerase chain reaction (RT-PCR) method capable of identifying two rt269 types in CHB genotype C2 patients.
METHODS We designed proper primer and probe sets for LNA-RT-PCR for the separation of rt269 types. Using synthesized DNAs of the wild type and variant forms, melting temperature analysis, detection sensitivity, and endpoint genotyping for LNA-RT-PCR were performed. The developed LNA-RT-PCR method was applied to a total of 94 CHB patients of genotype C2 for the identification of two rt269 polymorphisms, and these results were compared with those obtained by a direct sequencing protocol.
RESULTS The LNA-RT-PCR method could identify two rt269L and rt269I polymorphisms of three genotypes, two rt269L types [‘L1’ (WT) and ‘L2’] and one rt269I type (‘I’) in single (63 samples, 72.4%) or mixed forms (24 samples, 27.6%) in 87 (92.6% sensitivity) of 94 samples from Korean CHB patients. When the results were compared with those obtained by the direct sequencing protocol, the LNA-RT-PCR method showed the same results in all but one of 87 positive detected samples (98.9% specificity).
CONCLUSION The newly developed LNA-RT-PCR method could identify two rt269 polymorphisms, rt269L and rt269I, in CHB patients with genotype C2 infections. This method could be effectively used for the understanding of disease progression in genotype C2 endemic areas.
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Affiliation(s)
- Kijeong Kim
- Department of Microbiology, College of Medicine, Chung-Ang University, Seoul 06974, South Korea
| | - Yu-Min Choi
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul 03080, South Korea
| | - Dong Hyun Kim
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul 03080, South Korea
| | - Junghwa Jang
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul 03080, South Korea
| | - Won Hyeok Choe
- Department of Internal Medicine, Konkuk University School of Medicine, Seoul 05030, South Korea
| | - Bum-Joon Kim
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul 03080, South Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, South Korea
- Liver Research Institute, College of Medicine, Seoul National University, Seoul 03080, South Korea
- Seoul National University Medical Research Center, Seoul 03080, South Korea
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76
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Dobrowolska K, Zarębska-Michaluk D, Brzdęk M, Rzymski P, Rogalska M, Moniuszko-Malinowska A, Kozielewicz D, Hawro M, Rorat M, Sikorska K, Jaroszewicz J, Kowalska J, Flisiak R. Retrospective Analysis of the Effectiveness of Remdesivir in COVID-19 Treatment during Periods Dominated by Delta and Omicron SARS-CoV-2 Variants in Clinical Settings. J Clin Med 2023; 12:jcm12062371. [PMID: 36983370 PMCID: PMC10051185 DOI: 10.3390/jcm12062371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Continuous evaluation of real-world treatment effectiveness of COVID-19 medicines is required due to the ongoing evolution of SARS-CoV-2 and the possible emergence of resistance. Therefore, this study aimed to analyze, in a retrospective manner, the outcomes in patients hospitalized with COVID-19 during the pandemic waves dominated by Delta and Omicron variants and treated with remdesivir (RDV) (n = 762) in comparison to a demographically and clinically matched group not treated with any antivirals (n = 1060). A logistic regression analysis revealed that RDV treatment was associated with a significantly lower risk of death during both Delta wave (OR = 0.42, 95%CI: 0.29-0.60; p < 0.0001) and Omicron-dominated period (OR = 0.56, 95%CI: 0.35-0.92; p = 0.02). Moreover, RDV-treated groups were characterized by a lower percentage of patients requiring mechanical ventilation, but the difference was not statistically significant. This study is the first real-world evidence that RDV remains effective during the dominance of more pathogenic SARS-CoV-2 variants and those that cause a milder course of the disease, and continues to be an essential element of COVID-19 therapy.
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Affiliation(s)
| | - Dorota Zarębska-Michaluk
- Department of Infectious Diseases and Allergology, Jan Kochanowski University, 25-317 Kielce, Poland
- Department of Infectious Diseases, Provincial Hospital, 25-317 Kielce, Poland
| | - Michał Brzdęk
- Collegium Medicum, Jan Kochanowski University, 25-317 Kielce, Poland
| | - Piotr Rzymski
- Department of Environmental Medicine, Poznan University of Medical Sciences, 60-806 Poznań, Poland
| | - Magdalena Rogalska
- Department of Infectious Diseases and Hepatology, Medical University of Białystok, 15-540 Białystok, Poland
| | - Anna Moniuszko-Malinowska
- Department of Infectious Diseases and Neuroinfections, Medical University of Białystok, 15-809 Białystok, Poland
| | - Dorota Kozielewicz
- Department of Infectious Diseases and Hepatology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Marcin Hawro
- Department of Infectious Diseases and Hepatology, Medical Center in Łańcut, 37-100 Łańcut, Poland
| | - Marta Rorat
- Department of Forensic Medicine, Wrocław Medical University, 50-367 Wroclaw, Poland
| | - Katarzyna Sikorska
- Institute of Maritime and Tropical Medicine, Faculty of Health Sciences, Medical University of Gdansk, 81-519 Gdynia, Poland
| | - Jerzy Jaroszewicz
- Department of Infectious Diseases and Hepatology, Medical University of Silesia, 41-902 Katowice, Poland
| | - Justyna Kowalska
- Department of Adults' Infectious Diseases, Medical University of Warsaw, 01-201 Warsaw, Poland
| | - Robert Flisiak
- Department of Infectious Diseases and Hepatology, Medical University of Białystok, 15-540 Białystok, Poland
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77
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Song M, Hong S, Lee LP. Multiplexed Ultrasensitive Sample-to-Answer RT-LAMP Chip for the Identification of SARS-CoV-2 and Influenza Viruses. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2207138. [PMID: 36398425 DOI: 10.1002/adma.202207138] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/21/2022] [Indexed: 06/16/2023]
Abstract
Prompt on-site diagnosis of SARS-CoV-2 with other respiratory infections will have minimized the global impact of the COVID-19 pandemic through rapid, effective management. However, no such multiplex point-of-care (POC) chip has satisfied a suitable sensitivity of gold-standard nucleic acid amplification tests (NAATs). Here, a rapid multiplexed ultrasensitive sample-to-answer loop-mediated isothermal amplification (MUSAL) chip operated by simple LED-driven photothermal amplification to detect six targets from single-swab sampling is presented. First, the MUSAL chip allows ultrafast on-chip sample preparation with ≈500-fold preconcentration at a rate of 1.2 mL min-1 . Second, the chip enables contamination-free amplification using autonomous target elution into on-chip reagents by photothermal activation. Finally, the chip accomplishes multiplexed on-chip diagnostics of SARS-CoV-2 and influenza viruses with a limit of detection (LoD) of 0.5 copies µL-1 . The rapid, ultrasensitive, cost-effective sample-to-answer chip with a multiplex capability will allow timely management of various pandemics situations that may be faced shortly.
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Affiliation(s)
- Minsun Song
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
| | - SoonGweon Hong
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
| | - Luke P Lee
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University (SKKU), Suwon, Gyeonggi-do, 16419, Republic of Korea
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78
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Oliveira LS, Reyes A, Dutilh BE, Gruber A. Rational Design of Profile HMMs for Sensitive and Specific Sequence Detection with Case Studies Applied to Viruses, Bacteriophages, and Casposons. Viruses 2023; 15:519. [PMID: 36851733 PMCID: PMC9966878 DOI: 10.3390/v15020519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/01/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Profile hidden Markov models (HMMs) are a powerful way of modeling biological sequence diversity and constitute a very sensitive approach to detecting divergent sequences. Here, we report the development of protocols for the rational design of profile HMMs. These methods were implemented on TABAJARA, a program that can be used to either detect all biological sequences of a group or discriminate specific groups of sequences. By calculating position-specific information scores along a multiple sequence alignment, TABAJARA automatically identifies the most informative sequence motifs and uses them to construct profile HMMs. As a proof-of-principle, we applied TABAJARA to generate profile HMMs for the detection and classification of two viral groups presenting different evolutionary rates: bacteriophages of the Microviridae family and viruses of the Flavivirus genus. We obtained conserved models for the generic detection of any Microviridae or Flavivirus sequence, and profile HMMs that can specifically discriminate Microviridae subfamilies or Flavivirus species. In another application, we constructed Cas1 endonuclease-derived profile HMMs that can discriminate CRISPRs and casposons, two evolutionarily related transposable elements. We believe that the protocols described here, and implemented on TABAJARA, constitute a generic toolbox for generating profile HMMs for the highly sensitive and specific detection of sequence classes.
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Affiliation(s)
- Liliane S. Oliveira
- Department of Parasitology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63108, USA
| | - Bas E. Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, 07743 Jena, Germany
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Arthur Gruber
- Department of Parasitology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
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Hosaka Y, Yan Y, Naito T, Oyama R, Tsuchiya K, Yamamoto N, Nojiri S, Hori S, Takahashi K, Tabe Y. SARS-CoV-2 evolution among patients with immunosuppression in a nosocomial cluster of a Japanese medical center during the Delta (AY.29 sublineage) surge. Front Microbiol 2023; 14:944369. [PMID: 36846745 PMCID: PMC9947280 DOI: 10.3389/fmicb.2023.944369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 01/11/2023] [Indexed: 02/11/2023] Open
Abstract
Background Previous studies have shown that patients with immunosuppression tend to have longer-lasting SARS-CoV-2 infections and a number of mutations were observed during the infection period. However, these studies were, in general, conducted longitudinally. Mutation evolution among groups of patients with immunosuppression have not been well studied, especially among Asian populations. Methods Our study targeted a nosocomial cluster of SARS-CoV-2 infection in a Japanese medical center during Delta surge (AY.29 sublineage), involving ward nurses and inpatients. Whole-genome sequencing analyses were performed to examine mutation changes. Haplotype and minor variant analyses were furtherly performed to detect the mutations on the viral genomes in detail. In addition, sequences of the first wild-type strain hCoV-19/Wuhan/WIV04/2019 and AY.29 wild-type strain hCoV-19/Japan/TKYK15779/2021 were used as references to assess the phylogenetical development of this cluster. Results A total of 6 nurses and 14 inpatients were identified as a nosocomial cluster from September 14 through 28, 2021. All were Delta variant (AY.29 sublineage) positive. 92.9% of infected patients (13 out of 14) were either cancer patients and/or receiving immunosuppressive or steroid treatments. Compared to AY.29 wild type, a total of 12 mutations were found in the 20 cases. Haplotype analysis found one index group of eight cases with F274F (N) mutation and 10 other haplotypes with one to three additional mutations. Furthermore, we found that cases with more than three minor variants were all cancer patients under immunosuppressive treatments. The phylogenetical tree analysis, including 20 nosocomial cluster-associated viral genomes, the first wild-type strain and the AY.29 wild-type strain as references, indicated the mutation development of the AY.29 virus in this cluster. Conclusion Our study of a nosocomial SARS-CoV-2 cluster highlights mutation acquisition during transmission. More importantly, it provided new evidence emphasizing the need to further improve infection control measures to prevent nosocomial infection among immunosuppressed patients.
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Affiliation(s)
- Yoshie Hosaka
- Department of Clinical Laboratory Medicine, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Yan Yan
- Department of General Medicine, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Toshio Naito
- Department of General Medicine, Juntendo University Faculty of Medicine, Tokyo, Japan
- Department of Research Support Utilizing Bioresource Bank, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Rieko Oyama
- Department of Research Support Utilizing Bioresource Bank, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Koji Tsuchiya
- Department of Clinical Laboratory Medicine, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Norio Yamamoto
- Department of Microbiology, Tokai University School of Medicine, Hiratsuka, Kanagawa, Japan
| | - Shuko Nojiri
- Medical Technology Innovation Center, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Satoshi Hori
- Infection Control Unit, Juntendo University Hospital, Tokyo, Japan
| | - Kazuhiko Takahashi
- Department of Research Support Utilizing Bioresource Bank, Juntendo University Faculty of Medicine, Tokyo, Japan
- Department of Respiratory Medicine, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Yoko Tabe
- Department of Clinical Laboratory Medicine, Juntendo University Faculty of Medicine, Tokyo, Japan
- Department of Research Support Utilizing Bioresource Bank, Juntendo University Faculty of Medicine, Tokyo, Japan
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80
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Lewin AC, Hicks SK, Carter RT. A review of evidence-based management of infectious ocular surface disease in shelter-housed domestic cats. Vet Ophthalmol 2023; 26 Suppl 1:47-58. [PMID: 36749144 DOI: 10.1111/vop.13063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 02/08/2023]
Abstract
Infectious ocular surface disease (IOSD) is a common problem in shelter-housed domestic cats and has a widespread negative impact on animal welfare. While the common etiological agents are well-described, addressing IOSD in large groups of animals presents a management challenge to the clinician and logistical challenges to shelter employees. Treatments, diagnostics, and prevention strategies that are effective in privately owned or experimental animals may be impractical or ineffective in the shelter environment. This review article focuses on the relative prevalence of etiological agents in feline IOSD, practical diagnostic testing protocols, prevention strategies, and treatment of IOSD in shelter-housed cats. Discrepancies between experimental laboratory-based studies and clinical trials assessing therapeutics for treatment of feline herpes virus are highlighted. Further high-quality clinical trials are necessary to determine optimal preventative and therapeutic protocols for IOSD in shelter-housed cats.
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Affiliation(s)
- Andrew C Lewin
- Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Sarah K Hicks
- Shelter Medicine Program University of Wisconsin-Madison, School of Veterinary Medicine, Madison, Wisconsin, USA
| | - Renee T Carter
- Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
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81
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Wu C, Paradis NJ, Lakernick PM, Hryb M. L-shaped distribution of the relative substitution rate (c/μ) observed for SARS-COV-2's genome, inconsistent with the selectionist theory, the neutral theory and the nearly neutral theory but a near-neutral balanced selection theory: Implication on "neutralist-selectionist" debate. Comput Biol Med 2023; 153:106522. [PMID: 36638615 PMCID: PMC9814386 DOI: 10.1016/j.compbiomed.2022.106522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 12/17/2022] [Accepted: 12/31/2022] [Indexed: 01/07/2023]
Abstract
The genomic substitution rate (GSR) of SARS-CoV-2 exhibits a molecular clock feature and does not change under fluctuating environmental factors such as the infected human population (10°-107), vaccination etc. The molecular clock feature is believed to be inconsistent with the selectionist theory (ST). The GSR shows lack of dependence on the effective population size, suggesting Ohta's nearly neutral theory (ONNT) is not applicable to this virus. Big variation of the substitution rate within its genome is also inconsistent with Kimura's neutral theory (KNT). Thus, all three existing evolution theories fail to explain the evolutionary nature of this virus. In this paper, we proposed a Segment Substitution Rate Model (SSRM) under non-neutral selections and pointed out that a balanced mechanism between negative and positive selection of some segments that could also lead to the molecular clock feature. We named this hybrid mechanism as near-neutral balanced selection theory (NNBST) and examined if it was followed by SARS-CoV-2 using the three independent sets of SARS-CoV-2 genomes selected by the Nextstrain team. Intriguingly, the relative substitution rate of this virus exhibited an L-shaped probability distribution consisting with NNBST rather than Poisson distribution predicted by KNT or an asymmetric distribution predicted by ONNT in which nearly neutral sites are believed to be slightly deleterious only, or the distribution that is lack of nearly neutral sites predicted by ST. The time-dependence of the substitution rates for some segments and their correlation with the vaccination were observed, supporting NNBST. Our relative substitution rate method provides a tool to resolve the long standing "neutralist-selectionist" controversy. Implications of NNBST in resolving Lewontin's Paradox is also discussed.
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Affiliation(s)
- Chun Wu
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, 08028, USA; Department of Biological & Biomedical Sciences, Rowan University, Glassboro, NJ, 08028, USA.
| | - Nicholas J Paradis
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, 08028, USA
| | - Phillip M Lakernick
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, 08028, USA
| | - Mariya Hryb
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, 08028, USA
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82
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Mei R, Heng X, Liu X, Chen G. Glycopolymers for Antibacterial and Antiviral Applications. Molecules 2023; 28:molecules28030985. [PMID: 36770653 PMCID: PMC9919862 DOI: 10.3390/molecules28030985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/05/2023] [Accepted: 01/11/2023] [Indexed: 01/21/2023] Open
Abstract
Diseases induced by bacterial and viral infections are common occurrences in our daily life, and the main prevention and treatment strategies are vaccination and taking antibacterial/antiviral drugs. However, vaccines can only be used for specific viral infections, and the abuse of antibacterial/antiviral drugs will create multi-drug-resistant bacteria and viruses. Therefore, it is necessary to develop more targeted prevention and treatment methods against bacteria and viruses. Proteins on the surface of bacteria and viruses can specifically bind to sugar, so glycopolymers can be used as potential antibacterial and antiviral drugs. In this review, the research of glycopolymers for bacterial/viral detection/inhibition and antibacterial/antiviral applications in recent years are summarized.
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Affiliation(s)
- Ruoyao Mei
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
| | - Xingyu Heng
- Key Laboratory of Polymeric Material Design and Synthesis for Biomedical Function, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, 199 Ren−Ai Road, Suzhou 215123, China
| | - Xiaoli Liu
- Key Laboratory of Polymeric Material Design and Synthesis for Biomedical Function, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, 199 Ren−Ai Road, Suzhou 215123, China
- Correspondence: (X.L.); (G.C.)
| | - Gaojian Chen
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
- Key Laboratory of Polymeric Material Design and Synthesis for Biomedical Function, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, 199 Ren−Ai Road, Suzhou 215123, China
- Correspondence: (X.L.); (G.C.)
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83
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Chen NF, Chaguza C, Gagne L, Doucette M, Smole S, Buzby E, Hall J, Ash S, Harrington R, Cofsky S, Clancy S, Kapsak CJ, Sevinsky J, Libuit K, Park DJ, Hemarajata P, Garrigues JM, Green NM, Sierra-Patev S, Carpenter-Azevedo K, Huard RC, Pearson C, Incekara K, Nishimura C, Huang JP, Gagnon E, Reever E, Razeq J, Muyombwe A, Borges V, Ferreira R, Sobral D, Duarte S, Santos D, Vieira L, Gomes JP, Aquino C, Savino IM, Felton K, Bajwa M, Hayward N, Miller H, Naumann A, Allman R, Greer N, Fall A, Mostafa HH, McHugh MP, Maloney DM, Dewar R, Kenicer J, Parker A, Mathers K, Wild J, Cotton S, Templeton KE, Churchwell G, Lee PA, Pedrosa M, McGruder B, Schmedes S, Plumb MR, Wang X, Barcellos RB, Godinho FM, Salvato RS, Ceniseros A, Breban MI, Grubaugh ND, Gallagher GR, Vogels CB. Development of an amplicon-based sequencing approach in response to the global emergence of human monkeypox virus. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2022.10.14.22280783. [PMID: 36299420 PMCID: PMC9603838 DOI: 10.1101/2022.10.14.22280783] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The 2022 multi-country monkeypox (mpox) outbreak concurrent with the ongoing COVID-19 pandemic has further highlighted the need for genomic surveillance and rapid pathogen whole genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, these methods are resource intensive and require samples with high viral DNA concentrations. Given the atypical clinical presentation of cases associated with the outbreak and uncertainty regarding viral load across both the course of infection and anatomical body sites, there was an urgent need for a more sensitive and broadly applicable sequencing approach. Highly multiplexed amplicon-based sequencing (PrimalSeq) was initially developed for sequencing of Zika virus, and later adapted as the main sequencing approach for SARS-CoV-2. Here, we used PrimalScheme to develop a primer scheme for human monkeypox virus that can be used with many sequencing and bioinformatics pipelines implemented in public health laboratories during the COVID-19 pandemic. We sequenced clinical samples that tested presumptive positive for human monkeypox virus with amplicon-based and metagenomic sequencing approaches. We found notably higher genome coverage across the virus genome, with minimal amplicon drop-outs, in using the amplicon-based sequencing approach, particularly in higher PCR cycle threshold (lower DNA titer) samples. Further testing demonstrated that Ct value correlated with the number of sequencing reads and influenced the percent genome coverage. To maximize genome coverage when resources are limited, we recommend selecting samples with a PCR cycle threshold below 31 Ct and generating 1 million sequencing reads per sample. To support national and international public health genomic surveillance efforts, we sent out primer pool aliquots to 10 laboratories across the United States, United Kingdom, Brazil, and Portugal. These public health laboratories successfully implemented the human monkeypox virus primer scheme in various amplicon sequencing workflows and with different sample types across a range of Ct values. Thus, we show that amplicon based sequencing can provide a rapidly deployable, cost-effective, and flexible approach to pathogen whole genome sequencing in response to newly emerging pathogens. Importantly, through the implementation of our primer scheme into existing SARS-CoV-2 workflows and across a range of sample types and sequencing platforms, we further demonstrate the potential of this approach for rapid outbreak response.
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Affiliation(s)
- Nicholas F.G. Chen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Luc Gagne
- Massachusetts Department of Public Health, Boston, MA, USA
| | | | - Sandra Smole
- Massachusetts Department of Public Health, Boston, MA, USA
| | - Erika Buzby
- Massachusetts Department of Public Health, Boston, MA, USA
| | - Joshua Hall
- Massachusetts Department of Public Health, Boston, MA, USA
| | - Stephanie Ash
- Massachusetts Department of Public Health, Boston, MA, USA
| | | | - Seana Cofsky
- Massachusetts Department of Public Health, Boston, MA, USA
| | - Selina Clancy
- Massachusetts Department of Public Health, Boston, MA, USA
| | | | | | | | | | | | | | - Nicole M. Green
- Los Angeles County Public Health Laboratories, Downey, CA, USA
| | - Sean Sierra-Patev
- Rhode Island Department of Health, Rhode Island State Health Laboratory, Providence, RI, USA
| | | | - Richard C. Huard
- Rhode Island Department of Health, Rhode Island State Health Laboratory, Providence, RI, USA
| | - Claire Pearson
- Connecticut Department of Public Health, Rocky Hill, CT, USA
| | | | | | - Jian Ping Huang
- Connecticut Department of Public Health, Rocky Hill, CT, USA
| | - Emily Gagnon
- Connecticut Department of Public Health, Rocky Hill, CT, USA
| | - Ethan Reever
- Connecticut Department of Public Health, Rocky Hill, CT, USA
| | - Jafar Razeq
- Connecticut Department of Public Health, Rocky Hill, CT, USA
| | | | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Rita Ferreira
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniel Sobral
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Silvia Duarte
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniela Santos
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Luís Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal,Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Carly Aquino
- Delaware Public Health Laboratory, Smyrna, DE, USA
| | | | | | - Moneeb Bajwa
- Delaware Public Health Laboratory, Smyrna, DE, USA
| | | | - Holly Miller
- Delaware Public Health Laboratory, Smyrna, DE, USA
| | | | - Ria Allman
- Delaware Public Health Laboratory, Smyrna, DE, USA
| | - Neel Greer
- Delaware Public Health Laboratory, Smyrna, DE, USA
| | - Amary Fall
- Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Martin P. McHugh
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK,School of Medicine, University of St Andrews, St Andrews, UK
| | - Daniel M. Maloney
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK,Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Rebecca Dewar
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Juliet Kenicer
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Abby Parker
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Katharine Mathers
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Jonathan Wild
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Seb Cotton
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Kate E. Templeton
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - George Churchwell
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, FL, USA
| | - Philip A. Lee
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, FL, USA
| | - Maria Pedrosa
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, FL, USA
| | - Brenna McGruder
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, FL, USA
| | - Sarah Schmedes
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, FL, USA
| | - Matthew R. Plumb
- Minnesota Department of Health, Public Health Laboratory, St. Paul, MN, USA
| | - Xiong Wang
- Minnesota Department of Health, Public Health Laboratory, St. Paul, MN, USA
| | - Regina Bones Barcellos
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Fernanda M.S. Godinho
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Richard Steiner Salvato
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Glen R. Gallagher
- Massachusetts Department of Public Health, Boston, MA, USA,Rhode Island Department of Health, Rhode Island State Health Laboratory, Providence, RI, USA
| | - Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
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84
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Trancart S, Tweedie A, Liu O, Paul-Pont I, Hick P, Houssin M, Whittington RJ. Diversity and molecular epidemiology of Ostreid herpesvirus 1 in farmed Crassostrea gigas in Australia: Geographic clusters and implications for "microvariants" in global mortality events. Virus Res 2023; 323:198994. [PMID: 36332723 PMCID: PMC10194400 DOI: 10.1016/j.virusres.2022.198994] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 11/08/2022]
Abstract
Since 2010, mass mortality events known as Pacific oyster mortality syndrome (POMS) have occurred in Crassostrea gigas in Australia associated with Ostreid herpesvirus 1. The virus was thought to be an OsHV-1 µVar or "microvariant", i.e. one of the dominant variants associated with POMS in Europe, but there are few data to characterize the genotype in Australia. Consequently, the genetic identity and diversity of the virus was determined to understand the epidemiology of the disease in Australia. Samples were analysed from diseased C. gigas over five summer seasons between 2011 and 2016 in POMS-affected estuaries: Georges River in New South Wales (NSW), Hawkesbury River (NSW) and Pitt Water in Tasmania. Sequencing was attempted for six genomic regions. Numerous variants were identified among these regions (n = 100 isolates) while twelve variants were identified from concatenated nucleotide sequences (n = 61 isolates). Nucleotide diversity of the seven genotypes of C region among Australian isolates (Pi 0.99 × 10-3) was the lowest globally. All Australian isolates grouped in a cluster distinct from other OsHV-1 isolates worldwide. This is the first report that Australian outbreaks of POMS were associated with OsHV-1 distinct from OsHV-1 reference genotype, µVar and other microvariants from other countries. The findings illustrate that microvariants are not the only variants of OsHV-1 associated with mass mortality events in C. gigas. In addition, there was mutually exclusive spatial clustering of viral genomic and amino acid sequence variants between estuaries, and a possible association between genotype/amino acid sequence and the prevalence and severity of POMS, as this differed between these estuaries. The sequencing findings supported prior epidemiological evidence for environmental reservoirs of OsHV-1 for POMS outbreaks in Australia.
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Affiliation(s)
- Suzanne Trancart
- LABÉO Research Department, 1 Route de Rosel, Cedex 4, Caen 14053, France
| | - Alison Tweedie
- The University of Sydney, Sydney School of Veterinary Science, Faculty of Science, 425 Werombi Rd, Camden, NSW 2570, Australia; Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW 2568, Australia
| | - Olivia Liu
- The University of Sydney, Sydney School of Veterinary Science, Faculty of Science, 425 Werombi Rd, Camden, NSW 2570, Australia; Department of Agriculture, Water and the Environment, Canberra, ACT 2601, Australia
| | - Ika Paul-Pont
- The University of Sydney, Sydney School of Veterinary Science, Faculty of Science, 425 Werombi Rd, Camden, NSW 2570, Australia; LEMAR, Rue Dumont d'Urville, Plouzané 29280, France
| | - Paul Hick
- The University of Sydney, Sydney School of Veterinary Science, Faculty of Science, 425 Werombi Rd, Camden, NSW 2570, Australia; Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW 2568, Australia
| | - Maryline Houssin
- LABÉO Research Department, 1 Route de Rosel, Cedex 4, Caen 14053, France; UMR BOREA Université de Caen Normandie, MNHN, CNRS 8067, SU, IRD 207, UCN, UA, Esplanade de la Paix Caen Cedex 4 14032, France
| | - Richard J Whittington
- The University of Sydney, Sydney School of Veterinary Science, Faculty of Science, 425 Werombi Rd, Camden, NSW 2570, Australia.
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Mechanisms and Consequences of Genetic Variation in Hepatitis C Virus (HCV). Curr Top Microbiol Immunol 2023; 439:237-264. [PMID: 36592248 DOI: 10.1007/978-3-031-15640-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Chronic infection with hepatitis C virus (HCV) is an important contributor to the global incidence of liver diseases, including liver cirrhosis and hepatocellular carcinoma. Although common for single-stranded RNA viruses, HCV displays a remarkable high level of genetic diversity, produced primarily by the error-prone viral polymerase and host immune pressure. The high genetic heterogeneity of HCV has led to the evolution of several distinct genotypes and subtypes, with important consequences for pathogenesis, and clinical outcomes. Genetic variability constitutes an evasion mechanism against immune suppression, allowing the virus to evolve epitope escape mutants that avoid immune recognition. Thus, heterogeneity and variability of the HCV genome represent a great hindrance for the development of vaccines against HCV. In addition, the high genetic plasticity of HCV allows the virus to rapidly develop antiviral resistance mutations, leading to treatment failure and potentially representing a major hindrance for the cure of chronic HCV patients. In this chapter, we will present the central role that genetic diversity has in the viral life cycle and epidemiology of HCV. Incorporation errors and recombination, both the result of HCV polymerase activity, represent the main mechanisms of HCV evolution. The molecular details of both mechanisms have been only partially clarified and will be presented in the following sections. Finally, we will discuss the major consequences of HCV genetic diversity, namely its capacity to rapidly evolve antiviral and immunological escape variants that represent an important limitation for clearance of acute HCV, for treatment of chronic hepatitis C and for broadly protective vaccines.
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86
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Rana V, Chien E, Peng J, Milenkovic O. Small-Sample Estimation of the Mutational Support and Distribution of SARS-CoV-2. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:668-682. [PMID: 35385386 PMCID: PMC10009811 DOI: 10.1109/tcbb.2022.3165395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We consider the problem of determining the mutational support and distribution of the SARS-CoV-2 viral genome in the small-sample regime. The mutational support refers to the unknown number of sites that may eventually mutate in the SARS-CoV-2 genome while mutational distribution refers to the distribution of point mutations in the viral genome across a population. The mutational support may be used to assess the virulence of the virus and guide primer selection for real-time RT-PCR testing. Estimating the distribution of mutations in the genome of different subpopulations while accounting for the unseen may also aid in discovering new variants. To estimate the mutational support in the small-sample regime, we use GISAID sequencing data and our state-of-the-art polynomial estimation techniques based on new weighted and regularized Chebyshev approximation methods. For distribution estimation, we adapt the well-known Good-Turing estimator. Our analysis reveals several findings: First, the mutational supports exhibit significant differences in the ORF6 and ORF7a regions (older versus younger patients), ORF1b and ORF10 regions (females versus males) and in almost all ORFs (Asia/Europe/North America). Second, even though the N region of SARS-CoV-2 has a predicted 10% mutational support, mutations fall outside of the primer regions recommended by the CDC.
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87
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Xiao M, Ma F, Yu J, Xie J, Zhang Q, Liu P, Yu F, Jiang Y, Zhang L. A Computer Simulation of SARS-CoV-2 Mutation Spectra for Empirical Data Characterization and Analysis. Biomolecules 2022; 13:63. [PMID: 36671448 PMCID: PMC9855923 DOI: 10.3390/biom13010063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
It is very important to compute the mutation spectra, and simulate the intra-host mutation processes by sequencing data, which is not only for the understanding of SARS-CoV-2 genetic mechanism, but also for epidemic prediction, vaccine, and drug design. However, the current intra-host mutation analysis algorithms are not only inaccurate, but also the simulation methods are unable to quickly and precisely predict new SARS-CoV-2 variants generated from the accumulation of mutations. Therefore, this study proposes a novel accurate strand-specific SARS-CoV-2 intra-host mutation spectra computation method, develops an efficient and fast SARS-CoV-2 intra-host mutation simulation method based on mutation spectra, and establishes an online analysis and visualization platform. Our main results include: (1) There is a significant variability in the SARS-CoV-2 intra-host mutation spectra across different lineages, with the major mutations from G- > A, G- > C, G- > U on the positive-sense strand and C- > U, C- > G, C- > A on the negative-sense strand; (2) our mutation simulation reveals the simulation sequence starts to deviate from the base content percentage of Alpha-CoV/Delta-CoV after approximately 620 mutation steps; (3) 2019-NCSS provides an easy-to-use and visualized online platform for SARS-Cov-2 online analysis and mutation simulation.
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Affiliation(s)
- Ming Xiao
- College of Computer Science, Sichuan University, Chengdu 610065, China
- Med-X Center for Informatics, Sichuan University, Chengdu 610041, China
| | - Fubo Ma
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100049, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianghang Xie
- College of Computer Science, Sichuan University, Chengdu 610065, China
| | - Qiaozhen Zhang
- College of Computer Science, Sichuan University, Chengdu 610065, China
| | - Peng Liu
- National Wildlife Health Center, Hebei Agricultural University, Baoding 071001, China
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Hebei Agricultural University, Baoding 071001, China
| | - Fei Yu
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Hebei Agricultural University, Baoding 071001, China
- College of Life Sciences, Hebei Agricultural University, Baoding 071001, China
| | - Yuming Jiang
- College of Computer Science, Sichuan University, Chengdu 610065, China
| | - Le Zhang
- College of Computer Science, Sichuan University, Chengdu 610065, China
- Med-X Center for Informatics, Sichuan University, Chengdu 610041, China
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88
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An Emerging Lineage of Uropathogenic Extended Spectrum β-Lactamase Escherichia coli ST127. Microbiol Spectr 2022; 10:e0251122. [PMID: 36416548 PMCID: PMC9769692 DOI: 10.1128/spectrum.02511-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is one of the most common causes of urinary tract infections. Here, we report for the first time the whole-genome sequencing (WGS) and analysis of four extended-spectrum β-lactamase (ESBL), UPEC sequence type (ST) 127 isolates that were recovered from patients in five hospitals in Armenia from January to August of 2019. A phylogenetic comparison revealed that our isolates were closely related to each other by their core and accessory genomes, despite having been isolated from different regions and hospitals in Armenia. We identified unique genes in our isolates and in a closely related isolate recovered in France. The unique genes (hemolysin E virulence gene, lactate utilization operon lutABC, and endonuclease restriction modification operon hsdMSR) were identified in three separate genomic regions that were adjacent to prophage genes, including one region containing the TonB-dependent iron siderophore receptor gene ireA, which was only found in 5 other ST127 isolates from the European Nucleotide Archive (ENA). We further identified that these isolates possessed unique virulence and metabolic genes and harbored antibiotic resistance genes, including the ESBL genes blaCTX-M-3 (n = 3), blaCTX-M-236 (n = 1), and blaTEM-1 (n = 1), in addition to a quinolone resistance protein gene qnrD1 (n = 1), which was absent in the ST127 isolates obtained from the ENA. Moreover, a plasmid replicon gene IncI2 (n = 1) was unique to ARM88 of the Armenian isolates. Our findings demonstrate that at the time of this study, E. coli ST127 was a cause of urinary tract infections in patients in different regions of Armenia, with a possibility of cross-country transmission between Armenia and France. IMPORTANCE Whole-genome sequencing studies of pathogens causing infectious diseases are seriously lacking in Armenia, hampering global efforts to track, trace and contain infectious disease outbreaks. In this study, we report for the first-time the whole-genome sequencing and analysis of ESBL UPEC ST127 isolates recovered from hospitalized patients in Armenia and compare them with other E. coli ST127 retrieved from the ENA. We found close genetic similarities of the Armenian isolates, indicating that E. coli ST127 was potentially a dominant lineage causing urinary tract infections in Armenia. Furthermore, we identified unique genes that were horizontally acquired in the clusters of Armenian and French isolates that were absent in other ST127 isolates obtained from the ENA. Our findings highlight a possible cross-country transmission between Armenia and France and the idea that the implementation of WGS surveillance could contribute to global efforts in tackling antibiotic resistance, as bacteria carrying antimicrobial resistance (AMR) genes do not recognize borders.
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89
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Wilasang C, Suttirat P, Chadsuthi S, Wiratsudakul A, Modchang C. Competitive evolution of H1N1 and H3N2 influenza viruses in the United States: A mathematical modeling study. J Theor Biol 2022; 555:111292. [PMID: 36179800 DOI: 10.1016/j.jtbi.2022.111292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/17/2022] [Accepted: 09/21/2022] [Indexed: 01/14/2023]
Abstract
Seasonal influenza causes vast public health and economic impact globally. The prevention and control of the annual epidemics remain a challenge due to the antigenic evolution of the viruses. Here, we presented a novel modeling framework based on changes in amino acid sequences and relevant epidemiological data to retrospectively investigate the competitive evolution and transmission of H1N1 and H3N2 influenza viruses in the United States during October 2002 and April 2019. To do so, we estimated the time-varying disease transmission rate from the reported influenza cases and the time-varying antigenic change rate of the viruses from the changes in amino acid sequences. By incorporating the time-varying antigenic change rate into the transmission models, we found that the models could capture the evolutionary transmission dynamics of influenza viruses in the United States. Our modeling results also showed that the antigenic change of the virus plays an essential role in seasonal influenza dynamics.
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Affiliation(s)
- Chaiwat Wilasang
- Biophysics Group, Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Pikkanet Suttirat
- Biophysics Group, Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Sudarat Chadsuthi
- Department of Physics, Faculty of Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Anuwat Wiratsudakul
- Department of Clinical Sciences and Public Health, and the Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Charin Modchang
- Biophysics Group, Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Centre of Excellence in Mathematics, MHESI, Bangkok 10400, Thailand; Thailand Center of Excellence in Physics, Ministry of Higher Education, Science, Research and Innovation, 328 Si Ayutthaya Road, Bangkok 10400, Thailand.
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90
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Hong SJ, Park E, Jang YH, Shim JY, Park Y, Jin S, Guo S, Kim YJ, Son MJ, Chen L, Lim KI, Jung YM. Probe-Free Identification of RNA Virus Variants with Point Mutations by Surface-Enhanced Raman Spectroscopy. Anal Chem 2022; 94:17422-17430. [PMID: 36454685 DOI: 10.1021/acs.analchem.2c02912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
As observed in the COVID-19 pandemic, RNA viruses continue to rapidly evolve through mutations. In the absence of effective therapeutics, early detection of new severely pathogenic viruses and quarantine of infected people are critical for reducing the spread of the viral infections. However, conventional detection methods require a substantial amount of time to develop probes specific to new viruses, thereby impeding immediate response to the emergence of viral pathogens. In this study, we identified multiple types of viruses by obtaining the spectral fingerprint of their surface proteins with probe-free surface-enhanced Raman scattering (SERS). In addition, the SERS-based method can remarkably distinguish influenza virus variants with several surface protein point mutations from their parental strain. Principal component analysis (PCA) of the SERS spectra systematically captured the key Raman bands to distinguish the variants. Our results show that the combination of SERS and PCA can be a promising tool for rapid detection of newly emerging mutant viruses without a virus-specific probe.
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Affiliation(s)
- Su-Jin Hong
- Department of Chemical and Biological Engineering, Sookmyung Women's University, Seoul 04310, South Korea
| | - Eungyeong Park
- Department of Chemistry, Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon 24341, South Korea
| | - Yoon-Ha Jang
- Department of Chemical and Biological Engineering, Sookmyung Women's University, Seoul 04310, South Korea
| | - Ji-Yeon Shim
- Department of Chemical and Biological Engineering, Sookmyung Women's University, Seoul 04310, South Korea
| | - Yeonju Park
- Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon 24341, South Korea
| | - Sila Jin
- Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon 24341, South Korea
| | - Shuang Guo
- Department of Chemistry, Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon 24341, South Korea
| | - Yeon-Ju Kim
- Department of Chemical and Biological Engineering, Sookmyung Women's University, Seoul 04310, South Korea
| | - Min-Jeong Son
- Department of Chemical and Biological Engineering, Sookmyung Women's University, Seoul 04310, South Korea
| | - Lei Chen
- Key Laboratory of Preparation and Applications of Environmental Friendly Materials, Ministry of Education, College of Chemistry, Jilin Normal University, Changchun 130103, P.R. China
| | - Kwang-Il Lim
- Department of Chemical and Biological Engineering, Sookmyung Women's University, Seoul 04310, South Korea
| | - Young Mee Jung
- Department of Chemistry, Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon 24341, South Korea.,Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon 24341, South Korea
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91
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CRISPR/Cas technology: Opportunities for phytopathogenic viruses detection. J Biotechnol 2022; 360:211-217. [PMID: 36423792 DOI: 10.1016/j.jbiotec.2022.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 10/22/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022]
Abstract
Detection and monitoring of viruses are essential for healthy plants and prosperity. Recent development in CRISPR/Cas system in diagnosis has open an avenue well suited for pathogen detection. Variety of CRISPR associated proteins are being discovered, suggesting array of application and detection strategies in diagnosis. Phytopathogenic viruses are diverse with respect to their nucleic acid compositions, which presents a challenge in developing a single device applicable for almost all viruses. The review describes about the efficient use of CRISPR/Cas Technology in diagnosis, such as SHERLOCK, DETECTR and SATORI. These methods are different in their characteristic to identify specific nucleic acids and processing the detectable signals. These technologies are in their infancy and lot of scope is there to develop commercial kits. Plant tissue culture-based industries, climate control green houses, indoor cultivation facilities etc. has been considered as few examples. This review will be beneficial for researchers seeking to develop detection mechanism based on CRISPR/Cas technology. The outcome in the form of cost-effective detection of viruses will be boon for agro-based industries, which are facing challenges through virus contamination.
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92
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Hatmal MM, Al-Hatamleh MAI, Olaimat AN, Ahmad S, Hasan H, Ahmad Suhaimi NA, Albakri KA, Abedalbaset Alzyoud A, Kadir R, Mohamud R. Comprehensive literature review of monkeypox. Emerg Microbes Infect 2022; 11:2600-2631. [PMID: 36263798 PMCID: PMC9627636 DOI: 10.1080/22221751.2022.2132882] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/02/2022] [Indexed: 11/03/2022]
Abstract
The current outbreak of monkeypox (MPX) infection has emerged as a global matter of concern in the last few months. MPX is a zoonosis caused by the MPX virus (MPXV), which is one of the Orthopoxvirus species. Thus, it is similar to smallpox caused by the variola virus, and smallpox vaccines and drugs have been shown to be protective against MPX. Although MPX is not a new disease and is rarely fatal, the current multi-country MPX outbreak is unusual because it is occurring in countries that are not endemic for MPXV. In this work, we reviewed the extensive literature available on MPXV to summarize the available data on the major biological, clinical and epidemiological aspects of the virus and the important scientific findings. This review may be helpful in raising awareness of MPXV transmission, symptoms and signs, prevention and protective measures. It may also be of interest as a basis for performance of studies to further understand MPXV, with the goal of combating the current outbreak and boosting healthcare services and hygiene practices.Trial registration: ClinicalTrials.gov identifier: NCT02977715..Trial registration: ClinicalTrials.gov identifier: NCT03745131..Trial registration: ClinicalTrials.gov identifier: NCT00728689..Trial registration: ClinicalTrials.gov identifier: NCT02080767..
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Affiliation(s)
- Ma’mon M. Hatmal
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University, Zarqa, Jordan
| | | | - Amin N. Olaimat
- Department of Clinical Nutrition and Dietetics, Faculty of Applied Medical Sciences, The Hashemite University, Zarqa, Jordan
| | - Suhana Ahmad
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu, Malaysia
| | - Hanan Hasan
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman, Jordan
| | | | | | | | - Ramlah Kadir
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu, Malaysia
| | - Rohimah Mohamud
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu, Malaysia
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93
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Popovic M. Beyond COVID-19: Do biothermodynamic properties allow predicting the future evolution of SARS-CoV-2 variants? MICROBIAL RISK ANALYSIS 2022; 22:100232. [PMID: 36061411 PMCID: PMC9428117 DOI: 10.1016/j.mran.2022.100232] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/28/2022] [Accepted: 08/29/2022] [Indexed: 06/01/2023]
Abstract
During the COVID-19 pandemic, many statistical and epidemiological studies have been published, trying to predict the future development of the SARS-CoV-2 pandemic. However, it would be beneficial to have a specific, mechanistic biophysical model, based on the driving forces of processes performed during virus-host interactions and fundamental laws of nature, allowing prediction of future evolution of SARS-CoV-2 and other viruses. In this paper, an attempt was made to predict the development of the pandemic, based on biothermodynamic parameters: Gibbs energy of binding and Gibbs energy of growth. Based on analysis of biothermodynamic parameters of various variants of SARS-CoV-2, SARS-CoV and MERS-CoV that appeared during evolution, an attempt was made to predict the future directions of evolution of SARS-CoV-2 and potential occurrence of new strains that could lead to new pandemic waves. Possible new mutations that could appear in the future could lead to changes in chemical composition, biothermodynamic properties (driving forces of new virus strains) and biological properties of SARS CoV-2 that represent a risk for humanity.
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Affiliation(s)
- Marko Popovic
- School of Life Sciences, Technical University of Munich, Freising 85354 , Germany
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94
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Bloom JD, Beichman AC, Neher RA, Harris K. Evolution of the SARS-CoV-2 mutational spectrum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.11.19.517207. [PMID: 36451887 PMCID: PMC9709787 DOI: 10.1101/2022.11.19.517207] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
SARS-CoV-2 evolves rapidly in part because of its high mutation rate. Here we examine whether this mutational process itself has changed during viral evolution. To do this, we quantify the relative rates of different types of single nucleotide mutations at four-fold degenerate sites in the viral genome across millions of human SARS-CoV-2 sequences. We find clear shifts in the relative rates of several types of mutations during SARS-CoV-2 evolution. The most striking trend is a roughly two-fold decrease in the relative rate of G→T mutations in Omicron versus early clades, as was recently noted by Ruis et al (2022). There is also a decrease in the relative rate of C→T mutations in Delta, and other subtle changes in the mutation spectrum along the phylogeny. We speculate that these changes in the mutation spectrum could arise from viral mutations that affect genome replication, packaging, and antagonization of host innate-immune factors-although environmental factors could also play a role. Interestingly, the mutation spectrum of Omicron is more similar than that of earlier SARS-CoV-2 clades to the spectrum that shaped the long-term evolution of sarbecoviruses. Overall, our work shows that the mutation process is itself a dynamic variable during SARS-CoV-2 evolution, and suggests that human SARS-CoV-2 may be trending towards a mutation spectrum more similar to that of other animal sarbecoviruses.
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Affiliation(s)
- Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Annabel C Beichman
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, Washington, USA
| | - Richard A Neher
- Biozentrum, University of Basel, Basel, Switzerland, Swiss Institute of Bioinformatics, Lausanne, Switzerland
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95
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Geographical distribution of host's specific SARS-CoV-2 mutations in the early phase of the COVID-19 pandemic. Gene 2022; 851:147020. [PMCID: PMC9635256 DOI: 10.1016/j.gene.2022.147020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022]
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96
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Harding EF, Russo AG, Yan GJH, Mercer LK, White PA. Revealing the uncharacterised diversity of amphibian and reptile viruses. ISME COMMUNICATIONS 2022; 2:95. [PMID: 37938670 PMCID: PMC9723728 DOI: 10.1038/s43705-022-00180-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 08/18/2022] [Accepted: 09/15/2022] [Indexed: 06/29/2023]
Abstract
Amphibians and non-avian reptiles represent a significant proportion of terrestrial vertebrates, however knowledge of their viruses is not proportional to their abundance. Many amphibians and reptiles have strict habitual environments and localised populations and are vulnerable to viral outbreaks and potential elimination as a result. We sought to identify viruses that were hidden in amphibian and reptile metatranscriptomic data by screening 235 RNA-sequencing datasets from a 122 species covering 25 countries. We identified 26 novel viruses and eight previously characterised viruses from fifteen different viral families. Twenty-five viruses had RNA genomes with identity to Arteriviridae, Tobaniviridae, Hantaviridae, Rhabdoviridae, Astroviridae, Arenaviridae, Hepeviridae, Picornaviridae, Orthomyxoviridae, Reoviridae, Flaviviridae and Caliciviridae. In addition to RNA viruses, we also screened datasets for DNA viral transcripts, which are commonly excluded from transcriptomic analysis. We identified ten DNA viruses with identity to Papillomaviridae, Parvoviridae, Circoviridae and Adomaviridae. With the addition of these viruses, we expand the global amphibian and reptile virome and identify new potentially pathogenic viruses that could challenge populations. We speculate that amphibian viruses often have simpler genomes than those in amniotes, as in the case of the Secondpapillomavirinae and Orthomyxoviridae viruses identified in this study. In addition, we find evidence of inter-family recombination in RNA viruses, and we also identify new members of the recombinant Adomaviridae family. Overall, we provide insights into the uncharacterised diversity of amphibian and reptile viruses with the aim of improving population management, treatment and conservation into the future.
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Affiliation(s)
- Emma F Harding
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia
| | - Alice G Russo
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia
- Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Cancer Division, Sydney, NSW, 2010, Australia
| | - Grace J H Yan
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia
| | - Lewis K Mercer
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia
| | - Peter A White
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia.
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97
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Thompson JR. Analysis of the genome of grapevine red blotch virus and related grabloviruses indicates diversification prior to the arrival of Vitis vinifera in North America. J Gen Virol 2022; 103. [PMID: 36205485 DOI: 10.1099/jgv.0.001789] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study 163 complete whole-genome sequences of the emerging pathogen grapevine red blotch virus (GRBV; genus Grablovirus, family Geminiviridae) were used to reconstruct phylogenies using Bayesian analyses on time-tipped (heterochronous) data. Using different combinations of priors, Bayes factors identified heterochronous datasets (3×200 million chains) generated from strict clock and exponential tree priors as being the most robust. Substitution rates of 3.2×10-5 subsitutions per site per year (95% HPD 4.3-2.1×10-5) across the whole of the GRBV genome were estimated, suggesting ancestral GRBV diverged from ancestral wild Vitis latent virus 1 around 9 000 years ago, well before the first documented arrival of Vitis vinifera in North America. Whole-genome analysis of GRBV isolates in a single infected field-grown grapevine across 12 years identified 12 single nucleotide polymorphisms none of which were fixed substitutions: an observation not discordant with the in silico estimate. The substitution rate estimated here is lower than those estimated for other geminiviruses and is the first for a woody-host-infecting geminivirus.
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Affiliation(s)
- Jeremy R Thompson
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.,Present address: Plant Health and Environment Laboratory, Ministry for Primary Industries, Auckland 1140, New Zealand
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98
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Moghnieh R, El Hajj C, Abdallah D, Jbeily N, Bizri AR, Sayegh MH. Immunogenicity and Effectiveness of Primary and Booster Vaccine Combination Strategies during Periods of SARS-CoV-2 Delta and Omicron Variants. Vaccines (Basel) 2022; 10:1596. [PMID: 36298460 PMCID: PMC9607825 DOI: 10.3390/vaccines10101596] [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: 08/17/2022] [Revised: 09/12/2022] [Accepted: 09/16/2022] [Indexed: 11/22/2022] Open
Abstract
In this study involving a cohort of employees of the National Airline company in Lebanon, we assessed humoral immunity levels and the effectiveness of two COVID-19 vaccines, Gam-COVID-Vac versus BNT162b2, after two doses and after a homologous and heterologous BNT162b2 booster, in addition to the impact of hybrid immunity. Vaccine effectiveness (VE) was retrospectively determined against laboratory-confirmed SARS-CoV-2 infection during the periods of Delta and Omicron variants' predominance, separately, and was calculated based on a case-control study design. The humoral immune response, measured by a SARS-CoV-2 anti-spike receptor-binding domain (RBD) IgG titer, was prospectively assessed after the aforementioned vaccination schemes at different time points. This study showed higher effectiveness of BNT162b2 after two doses (81%) compared to two doses of Gam-COVID-Vac (41.8%) against the Delta variant of SARS-CoV-2, which correlated with anti-spike antibody levels. Regarding the Omicron variant, protection against infection and antibody levels were severely compromised and the correlation between an anti-spike IgG titer and effectiveness was lost, unlike the situation during the Delta wave. Considering the booster vaccination schemes, a homologous BNT162b2 booster after a BNT162b2 primary vaccination induced a higher humoral immune response when compared to that induced by a heterologous BNT162b2 booster after a Gam-COVID-Vac primary vaccination. However, the VE of both booster regimens against the Omicron variant was almost equal (64% in the homologous regimen and 57% in heterologous regimen). Hybrid immunity evidenced a better humoral response and a greater and longer protection against Delta and Omicron infections compared to vaccination-induced immunity in COVID-19-naïve individuals. Finally, the findings show that VE waned with time during the same wave, highlighting the importance of reinforcing primary and booster COVID-19 vaccination mainly at the beginning of each wave during the surge of a new variant of concern.
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Affiliation(s)
- Rima Moghnieh
- Division of Infectious Diseases, Department of Internal Medicine, Makassed General Hospital, Beirut P.O. Box 11-6301, Lebanon
- Faculty of Medicine, Lebanese University, Beirut P.O. Box 6573/14, Lebanon
| | - Claude El Hajj
- Faculty of Medicine, Lebanese University, Beirut P.O. Box 6573/14, Lebanon
- Middle East Airlines-AIRLIBAN S.A.L., Beirut P.O. Box 206, Lebanon
| | - Dania Abdallah
- Pharmacy Department, Makassed General Hospital, Beirut P.O. Box 11-6301, Lebanon
| | - Nayla Jbeily
- FMPS Holding S.A.L., Beirut P.O. Box 60 247, Lebanon
| | - Abdul Rahman Bizri
- Department of Internal Medicine, Division of Infectious Diseases, American University of Beirut Medical Center, Beirut P.O. Box 11-0236, Lebanon
| | - Mohamed H. Sayegh
- GAP Solutions under Contract No. 75N93019D00026 with National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, United States of America, Washington, DC 20201, USA
- Faculty of Medicine, American University of Beirut, Beirut P.O. Box 11-0236, Lebanon
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99
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Faleye TO, Skidmore PT, Elyaderani A, Smith A, Kaiser N, Adhikari S, Yanez A, Perleberg T, Driver EM, Halden RU, Varsani A, Scotch M. Canine picornaviruses detected in wastewater in Arizona, USA 2019 and 2021. INFECTION, GENETICS AND EVOLUTION 2022; 103:105315. [PMID: 35714764 PMCID: PMC9482372 DOI: 10.1016/j.meegid.2022.105315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 11/07/2022]
Abstract
Virus surveillance by wastewater-based epidemiology (WBE) in two Arizona municipalities in Maricopa County, USA (~700,000 people), revealed the presence of six canine picornavirus (CanPV) variants: five in 2019 and one in 2021. Phylogenetic analysis suggests these viruses might be from domestic dog breeds living within or around the area. Phylogenetic and pairwise identity analyses suggest over 15 years of likely enzootic circulation of multiple lineages of CanPV in the USA and possibly globally. Considering <10 CanPV sequences are publicly available in GenBank as of June 2, 2022, the results provided here constitute an increase of current knowledge on CanPV diversity and highlight the need for increased surveillance.
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100
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Campagnola G, Govindarajan V, Pelletier A, Canard B, Peersen OB. The SARS-CoV nsp12 Polymerase Active Site Is Tuned for Large-Genome Replication. J Virol 2022; 96:e0067122. [PMID: 35924919 PMCID: PMC9400494 DOI: 10.1128/jvi.00671-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/06/2022] [Indexed: 01/18/2023] Open
Abstract
Positive-strand RNA viruses replicate their genomes using virally encoded RNA-dependent RNA polymerases (RdRP) with a common active-site structure and closure mechanism upon which replication speed and fidelity can evolve to optimize virus fitness. Coronaviruses (CoV) form large multicomponent RNA replication-transcription complexes containing a core RNA synthesis machine made of the nsp12 RdRP protein with one nsp7 and two nsp8 proteins as essential subunits required for activity. We show that assembly of this complex can be accelerated 5-fold by preincubation of nsp12 with nsp8 and further optimized with the use of a novel nsp8L7 heterodimer fusion protein construct. Using rapid kinetics methods, we measure elongation rates of up to 260 nucleotides (nt)/s for the core replicase, a rate that is unusually fast for a viral polymerase. To address the origin of this fast rate, we examined the roles of two CoV-specific residues in the RdRP active site: Ala547, which replaces a conserved glutamate above the bound NTP, and Ser759, which mutates the palm domain GDD sequence to SDD. Our data show that Ala547 allows for a doubling of replication rate, but this comes at a fidelity cost that is mitigated by using a SDD sequence in the palm domain. Our biochemical data suggest that fixation of mutations in polymerase motifs F and C played a key role in nidovirus evolution by tuning replication rate and fidelity to accommodate their large genomes. IMPORTANCE Replicating large genomes represents a challenge for RNA viruses because fast RNA synthesis is needed to escape innate immunity defenses, but faster polymerases are inherently low-fidelity enzymes. Nonetheless, the coronaviruses replicate their ≈30-kb genomes using the core polymerase structure and mechanism common to all positive-strand RNA viruses. The classic explanation for their success is that the large-genome nidoviruses have acquired an exonuclease-based repair system that compensates for the high polymerase mutation rate. In this work, we establish that the nidoviral polymerases themselves also play a key role in maintaining genome integrity via mutations at two key active-site residues that enable very fast replication rates while maintaining typical mutation rates. Our findings further demonstrate the evolutionary plasticity of the core polymerase platform by showing how it has adapted during the expansion from short-genome picornaviruses to long-genome nidoviruses.
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Affiliation(s)
- Grace Campagnola
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Vishnu Govindarajan
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Annelise Pelletier
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Bruno Canard
- Centre National de la Recherche Scientifique, Aix-Marseille Université CNRS UMR 7257, AFMB, Marseille, France
| | - Olve B. Peersen
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
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