1
|
Wang C, Yu Q, Zheng S, Shen W, Li J, Xu C, Gu B. Phenylboronic Acid-Modified Membrane-Like Magnetic Quantum Dots Enable the Ultrasensitive and Broad-Spectrum Detection of Viruses by Lateral Flow Immunoassay. ACS NANO 2024; 18:16752-16765. [PMID: 38901038 DOI: 10.1021/acsnano.4c01824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Although lateral flow immunochromatographic assay (LFIA) is an effective point-of-care testing technology, it still cannot achieve broad-spectrum and ultrasensitive detection of viruses. Herein, we propose a multiplex LFIA platform using a two-dimensional graphene oxide (GO)-based magnetic fluorescent nanofilm (GF@DQD) as a multifunctional probe and 4-aminophenylboronic acid (APBA) as a broad-spectrum recognition molecule for viral glycoprotein detection. GF@DQD-APBA with enhanced magnetic/fluorescence properties and universal capture ability for multiple viruses was easily prepared through the electrostatic adsorption of one layer of density-controlled Fe3O4 nanoparticles (NPs) and thousands of small CdSe/ZnS-MPA quantum dots (QDs) on a monolayer GO sheet followed by chemical coupling with APBA on the QD surface. The GF@DQD-APBA probe enabled the universal capture and specific determination of different target viruses on the test strip through an arbitrary combination with the antibody-modified LFIA strip, thus greatly improving detection efficiency and reducing the cost and difficulty of multiplex LFIA for viruses. The proposed technique can simultaneously and sensitively diagnose three newly emerged viruses within 20 min with detection limits down to the pg/mL level. The excellent practicability of GF@DQD-APBA-LFIA was also demonstrated in the detection of 34 clinical specimens positive for SARS-CoV-2, revealing its potential for epidemic control and on-site viral detection.
Collapse
Affiliation(s)
- Chongwen Wang
- Department of Clinical Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510000, China
| | - Qing Yu
- Department of Clinical Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510000, China
| | - Shuai Zheng
- Department of Clinical Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510000, China
| | - Wanzhu Shen
- Department of Clinical Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510000, China
| | - Jiaxuan Li
- Department of Clinical Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510000, China
| | - Changyue Xu
- Department of Clinical Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510000, China
| | - Bing Gu
- Department of Clinical Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510000, China
| |
Collapse
|
2
|
Zeng Z, Zhang Q, Ye F, Dang X, Jiang X, Lv G, Wang X, Peng H, Fang D, Xiao H, Zhang Y, Wu G, Mao J, Ahmad M, Deng S. Bioprotective Respirator Assembled by Defective Carbon Nitride for Long-Term Light Triggered Health Protection. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2403098. [PMID: 38898726 DOI: 10.1002/advs.202403098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 05/16/2024] [Indexed: 06/21/2024]
Abstract
Wearing face masks is the best way to stop the spread of respiratory infections. However, if masks are not sterilized, changing them too frequently can actually increase the risk of cross-contamination. Herein, the construction of an antipathogen photocatalytic mask with carbon vacancy-modified carbon nitride nanosheets (g-C3N4-VC Ns) coated on the non-woven fabrics of the out layer of the mask, offering effective and long-term protection against damaging pathogens when exposed to light is reported. The introduced carbon vacancies are found capable of creating energy-disordered sites and inducing energetic electric force to overcome the Coulomb interactions between electron-hole pairs, thus promoting the electron-hole separation to achieve a high generation of reactive oxygen species (ROS). Thanks to its high activity in generating ROS upon exposure to light, the as-prepared photocatalytic mask shows high pathogen sterilization performance. This, in turn, prolongs the mask's protective lifetime, decreases the need for regular replacement, and decreases medical waste production. The work demonstrated here opens new viewpoints in designing pathogens biocidal protective devices for health protection, offering significant promise in specific environment self-protection.
Collapse
Affiliation(s)
- Zhenxing Zeng
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu, 611130, P. R. China
- Sichuan Provincial Engineering Center of Agricultural Environmental Pollution Control, Chengdu, 611130, P. R. China
| | - Qi Zhang
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu, 611130, P. R. China
- Sichuan Provincial Engineering Center of Agricultural Environmental Pollution Control, Chengdu, 611130, P. R. China
| | - Fei Ye
- Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao, 066004, P. R. China
| | - Xueming Dang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, P. R. China
| | - Xin Jiang
- School of Environment and Energy, Jiangxi Modern Polytechnic College, Nanchang, 330095, P. R. China
| | - Guochun Lv
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu, 611130, P. R. China
| | - Xiaojing Wang
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu, 611130, P. R. China
- Sichuan Provincial Engineering Center of Agricultural Environmental Pollution Control, Chengdu, 611130, P. R. China
| | - Hong Peng
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu, 611130, P. R. China
| | - Dexin Fang
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu, 611130, P. R. China
| | - Hong Xiao
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu, 611130, P. R. China
| | - Yanzong Zhang
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu, 611130, P. R. China
| | - Ganxue Wu
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu, 611130, P. R. China
| | - Jie Mao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, P. R. China
| | - Munir Ahmad
- Institute of Carbon Neutrality, Zhejiang Wanli University, Ningbo, 315100, P. R. China
| | - Shihuai Deng
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu, 611130, P. R. China
- Sichuan Provincial Engineering Center of Agricultural Environmental Pollution Control, Chengdu, 611130, P. R. China
| |
Collapse
|
3
|
Cuomo-Dannenburg G, McCain K, McCabe R, Unwin HJT, Doohan P, Nash RK, Hicks JT, Charniga K, Geismar C, Lambert B, Nikitin D, Skarp J, Wardle J, Kont M, Bhatia S, Imai N, van Elsland S, Cori A, Morgenstern C. Marburg virus disease outbreaks, mathematical models, and disease parameters: a systematic review. THE LANCET. INFECTIOUS DISEASES 2024; 24:e307-e317. [PMID: 38040006 PMCID: PMC7615873 DOI: 10.1016/s1473-3099(23)00515-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/03/2023] [Accepted: 08/03/2023] [Indexed: 12/03/2023]
Abstract
The 2023 Marburg virus disease outbreaks in Equatorial Guinea and Tanzania highlighted the importance of better understanding this lethal pathogen. We did a systematic review (PROSPERO CRD42023393345) of peer-reviewed articles reporting historical outbreaks, modelling studies, and epidemiological parameters focused on Marburg virus disease. We searched PubMed and Web of Science from database inception to March 31, 2023. Two reviewers evaluated all titles and abstracts with consensus-based decision making. To ensure agreement, 13 (31%) of 42 studies were double-extracted and a custom-designed quality assessment questionnaire was used for risk of bias assessment. We present detailed information on 478 reported cases and 385 deaths from Marburg virus disease. Analysis of historical outbreaks and seroprevalence estimates suggests the possibility of undetected Marburg virus disease outbreaks, asymptomatic transmission, or cross-reactivity with other pathogens, or a combination of these. Only one study presented a mathematical model of Marburg virus transmission. We estimate an unadjusted, pooled total random effect case fatality ratio of 61·9% (95% CI 38·8-80·6; I2=93%). We identify epidemiological parameters relating to transmission and natural history, for which there are few estimates. This systematic review and the accompanying database provide a comprehensive overview of Marburg virus disease epidemiology and identify key knowledge gaps, contributing crucial information for mathematical models to support future Marburg virus disease epidemic responses.
Collapse
Affiliation(s)
- Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Kelly McCain
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Ruth McCabe
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK; Department of Statistics, University of Oxford, Oxford, UK; Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - H Juliette T Unwin
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Patrick Doohan
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Rebecca K Nash
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Joseph T Hicks
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Kelly Charniga
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Cyril Geismar
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK; Health Protection Research Unit in Modelling and Health Economics, Imperial College London, London, UK
| | - Ben Lambert
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, UK
| | - Dariya Nikitin
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Janetta Skarp
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Jack Wardle
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Mara Kont
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Sangeeta Bhatia
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK; Health Protection Research Unit in Modelling and Health Economics, Imperial College London, London, UK; Modelling and Economics Unit, UK Health Security Agency, London, UK
| | - Natsuko Imai
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Sabine van Elsland
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Anne Cori
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK; Health Protection Research Unit in Modelling and Health Economics, Imperial College London, London, UK
| | - Christian Morgenstern
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK.
| |
Collapse
|
4
|
Wong W, Schaffner SF, Thwing J, Seck MC, Gomis J, Diedhiou Y, Sy N, Ndiop M, Ba F, Diallo I, Sene D, Diallo MA, Ndiaye YD, Sy M, Sene A, Sow D, Dieye B, Tine A, Ribado J, Suresh J, Lee A, Battle KE, Proctor JL, Bever CA, MacInnis B, Ndiaye D, Hartl DL, Wirth DF, Volkman SK. Evaluating the performance of Plasmodium falciparum genetic metrics for inferring National Malaria Control Programme reported incidence in Senegal. Malar J 2024; 23:68. [PMID: 38443939 PMCID: PMC10916253 DOI: 10.1186/s12936-024-04897-z] [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: 10/30/2023] [Accepted: 02/29/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Genetic surveillance of the Plasmodium falciparum parasite shows great promise for helping National Malaria Control Programmes (NMCPs) assess parasite transmission. Genetic metrics such as the frequency of polygenomic (multiple strain) infections, genetic clones, and the complexity of infection (COI, number of strains per infection) are correlated with transmission intensity. However, despite these correlations, it is unclear whether genetic metrics alone are sufficient to estimate clinical incidence. METHODS This study examined parasites from 3147 clinical infections sampled between the years 2012-2020 through passive case detection (PCD) across 16 clinic sites spread throughout Senegal. Samples were genotyped with a 24 single nucleotide polymorphism (SNP) molecular barcode that detects parasite strains, distinguishes polygenomic (multiple strain) from monogenomic (single strain) infections, and identifies clonal infections. To determine whether genetic signals can predict incidence, a series of Poisson generalized linear mixed-effects models were constructed to predict the incidence level at each clinical site from a set of genetic metrics designed to measure parasite clonality, superinfection, and co-transmission rates. RESULTS Model-predicted incidence was compared with the reported standard incidence data determined by the NMCP for each clinic and found that parasite genetic metrics generally correlated with reported incidence, with departures from expected values at very low annual incidence (< 10/1000/annual [‰]). CONCLUSIONS When transmission is greater than 10 cases per 1000 annual parasite incidence (annual incidence > 10‰), parasite genetics can be used to accurately infer incidence and is consistent with superinfection-based hypotheses of malaria transmission. When transmission was < 10‰, many of the correlations between parasite genetics and incidence were reversed, which may reflect the disproportionate impact of importation and focal transmission on parasite genetics when local transmission levels are low.
Collapse
Affiliation(s)
- Wesley Wong
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Stephen F Schaffner
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Julie Thwing
- Malaria Branch, Division of Parasitic Diseases and Malaria, Global Health Center, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mame Cheikh Seck
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Jules Gomis
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Younouss Diedhiou
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Ngayo Sy
- Section de Lutte Anti-Parasitaire (SLAP) Clinic, Thies, Senegal
| | - Medoune Ndiop
- Programme National de Lutte contre le Paludisme (PNLP), Dakar, Senegal
| | - Fatou Ba
- Programme National de Lutte contre le Paludisme (PNLP), Dakar, Senegal
| | - Ibrahima Diallo
- Programme National de Lutte contre le Paludisme (PNLP), Dakar, Senegal
| | - Doudou Sene
- Programme National de Lutte contre le Paludisme (PNLP), Dakar, Senegal
| | - Mamadou Alpha Diallo
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Yaye Die Ndiaye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Mouhamad Sy
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Aita Sene
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Djiby Sow
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Baba Dieye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Abdoulaye Tine
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Jessica Ribado
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Joshua Suresh
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Albert Lee
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Katherine E Battle
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Joshua L Proctor
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Caitlin A Bever
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Bronwyn MacInnis
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Daouda Ndiaye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Sarah K Volkman
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA.
- College of Natural, Behavioral, and Health Sciences, Simmons University, Boston, MA, USA.
| |
Collapse
|
5
|
Riesle-Sbarbaro SA, Wibbelt G, Düx A, Kouakou V, Bokelmann M, Hansen-Kant K, Kirchoff N, Laue M, Kromarek N, Lander A, Vogel U, Wahlbrink A, Wozniak DM, Scott DP, Prescott JB, Schaade L, Couacy-Hymann E, Kurth A. Selective replication and vertical transmission of Ebola virus in experimentally infected Angolan free-tailed bats. Nat Commun 2024; 15:925. [PMID: 38297087 PMCID: PMC10830451 DOI: 10.1038/s41467-024-45231-0] [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: 09/04/2023] [Accepted: 01/16/2024] [Indexed: 02/02/2024] Open
Abstract
The natural reservoir of Ebola virus (EBOV), agent of a zoonosis burdening several African countries, remains unidentified, albeit evidence points towards bats. In contrast, the ecology of the related Marburg virus is much better understood; with experimental infections of bats being instrumental for understanding reservoir-pathogen interactions. Experiments have focused on elucidating reservoir competence, infection kinetics and specifically horizontal transmission, although, vertical transmission plays a key role in many viral enzootic cycles. Herein, we investigate the permissiveness of Angolan free-tailed bats (AFBs), known to harbour Bombali virus, to other filoviruses: Ebola, Marburg, Taï Forest and Reston viruses. We demonstrate that only the bats inoculated with EBOV show high and disseminated viral replication and infectious virus shedding, without clinical disease, while the other filoviruses fail to establish productive infections. Notably, we evidence placental-specific tissue tropism and a unique ability of EBOV to traverse the placenta, infect and persist in foetal tissues of AFBs, which results in distinct genetic signatures of adaptive evolution. These findings not only demonstrate plausible routes of horizontal and vertical transmission in these bats, which are expectant of reservoir hosts, but may also reveal an ancillary transmission mechanism, potentially required for the maintenance of EBOV in small reservoir populations.
Collapse
Affiliation(s)
- S A Riesle-Sbarbaro
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - G Wibbelt
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - A Düx
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
- Helmholtz Institute for One Health, Greifswald, Germany
| | - V Kouakou
- LANADA, Laboratoire National d'Appui au Développement Agricole, Bingerville, Côte d'Ivoire
| | - M Bokelmann
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - K Hansen-Kant
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - N Kirchoff
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - M Laue
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - N Kromarek
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - A Lander
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - U Vogel
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - A Wahlbrink
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - D M Wozniak
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
- Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
| | - D P Scott
- Rocky Mountain Laboratories, National Institutes of Health, Hamilton, MT, USA
| | - J B Prescott
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - L Schaade
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - E Couacy-Hymann
- LANADA, Laboratoire National d'Appui au Développement Agricole, Bingerville, Côte d'Ivoire
- Centre National de Recherches Agronomiques, LIRED, Abidjan, Côte d'Ivoire
| | - A Kurth
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany.
| |
Collapse
|
6
|
Fang J, Zhou ZJ, Yuan S, Qiu Y, Ge XY. Lineage classification and selective site identification of Orthoebolavirus zairense. Microbes Infect 2024:105304. [PMID: 38278475 DOI: 10.1016/j.micinf.2024.105304] [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: 11/23/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 01/28/2024]
Abstract
As the high pathogenic species of Filoviridae virus family, Orthoebolavirus zairense (EBOV) shows frequent outbreaks in human in recently years since its first emerging in 1976 in Democratic Republic of the Congo (COD), bringing ongoing risks and burden on public health safety. Here, the phylogenetic relationship among major outbreaks was analyzed. The results showed that EBOV isolates could be divided into four lineages according to spatial and temporal epidemics. Then, the positive selection sites (PSSs) were detected on all proteins of the EBOV, exhibiting lineage characteristic. Particularly, sites in GP and VP24 were identified to be significantly under positive selection, and partial of which were maintained in the latest isolates in 2021. GP and L were found to have high variability between lineages. Substitutions including F443L and F443S in GP, as well as F1610L and I1951V in L could be characteristic of the two large outbreaks in COD (2018) and West Africa (2014), respectively. Further, substitutions of significant PSSs in VP24 and L proteins were visualized for analysis of structural changes, which may affect EBOV pathogenesis. In summary, our results gains insights in genetic characteristic and adaptive evolution of EBOV, which could facilitate gene functional research against EBOV.
Collapse
Affiliation(s)
- Jie Fang
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan, 410012, China
| | - Zhi-Jian Zhou
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan, 410012, China
| | - Shuofeng Yuan
- Department of Microbiology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ye Qiu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan, 410012, China
| | - Xing-Yi Ge
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan, 410012, China.
| |
Collapse
|
7
|
Guo C, Wu JY. Pathogen Discovery in the Post-COVID Era. Pathogens 2024; 13:51. [PMID: 38251358 PMCID: PMC10821006 DOI: 10.3390/pathogens13010051] [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: 11/11/2023] [Revised: 12/22/2023] [Accepted: 01/03/2024] [Indexed: 01/23/2024] Open
Abstract
Pathogen discovery plays a crucial role in the fields of infectious diseases, clinical microbiology, and public health. During the past four years, the global response to the COVID-19 pandemic highlighted the importance of early and accurate identification of novel pathogens for effective management and prevention of outbreaks. The post-COVID era has ushered in a new phase of infectious disease research, marked by accelerated advancements in pathogen discovery. This review encapsulates the recent innovations and paradigm shifts that have reshaped the landscape of pathogen discovery in response to the COVID-19 pandemic. Primarily, we summarize the latest technology innovations, applications, and causation proving strategies that enable rapid and accurate pathogen discovery for both acute and historical infections. We also explored the significance and the latest trends and approaches being employed for effective implementation of pathogen discovery from various clinical and environmental samples. Furthermore, we emphasize the collaborative nature of the pandemic response, which has led to the establishment of global networks for pathogen discovery.
Collapse
Affiliation(s)
- Cheng Guo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Jian-Yong Wu
- School of Public Health, Xinjiang Medical University, Urumqi 830017, China
| |
Collapse
|
8
|
Guttieres D, Diepvens C, Decouttere C, Vandaele N. Modeling Supply and Demand Dynamics of Vaccines against Epidemic-Prone Pathogens: Case Study of Ebola Virus Disease. Vaccines (Basel) 2023; 12:24. [PMID: 38250837 PMCID: PMC10819028 DOI: 10.3390/vaccines12010024] [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: 11/10/2023] [Revised: 12/13/2023] [Accepted: 12/22/2023] [Indexed: 01/23/2024] Open
Abstract
Health emergencies caused by epidemic-prone pathogens (EPPs) have increased exponentially in recent decades. Although vaccines have proven beneficial, they are unavailable for many pathogens. Furthermore, achieving timely and equitable access to vaccines against EPPs is not trivial. It requires decision-makers to capture numerous interrelated factors across temporal and spatial scales, with significant uncertainties, variability, delays, and feedback loops that give rise to dynamic and unexpected behavior. Therefore, despite progress in filling R&D gaps, the path to licensure and the long-term viability of vaccines against EPPs continues to be unclear. This paper presents a quantitative system dynamics modeling framework to evaluate the long-term sustainability of vaccine supply under different vaccination strategies. Data from both literature and 50 expert interviews are used to model the supply and demand of a prototypical Ebolavirus Zaire (EBOV) vaccine. Specifically, the case study evaluates dynamics associated with proactive vaccination ahead of an outbreak of similar magnitude as the 2018-2020 epidemic in North Kivu, Democratic Republic of the Congo. The scenarios presented demonstrate how uncertainties (e.g., duration of vaccine-induced protection) and design criteria (e.g., priority geographies and groups, target coverage, frequency of boosters) lead to important tradeoffs across policy aims, public health outcomes, and feasibility (e.g., technical, operational, financial). With sufficient context and data, the framework provides a foundation to apply the model to a broad range of additional geographies and priority pathogens. Furthermore, the ability to identify leverage points for long-term preparedness offers directions for further research.
Collapse
Affiliation(s)
- Donovan Guttieres
- Access-to-Medicines Research Centre, Faculty of Economics & Business, KU Leuven, 3000 Leuven, Belgium; (C.D.); (C.D.); (N.V.)
| | | | | | | |
Collapse
|
9
|
Weber A, Översti S, Kühnert D. Reconstructing relative transmission rates in Bayesian phylodynamics: Two-fold transmission advantage of Omicron in Berlin, Germany during December 2021. Virus Evol 2023; 9:vead070. [PMID: 38107332 PMCID: PMC10725310 DOI: 10.1093/ve/vead070] [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: 08/17/2023] [Revised: 11/08/2023] [Accepted: 11/27/2023] [Indexed: 12/19/2023] Open
Abstract
Phylodynamic methods have lately played a key role in understanding the spread of infectious diseases. During the coronavirus disease (COVID-19) pandemic, large scale genomic surveillance has further increased the potential of dynamic inference from viral genomes. With the continual emergence of novel severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) variants, explicitly allowing transmission rate differences between simultaneously circulating variants in phylodynamic inference is crucial. In this study, we present and empirically validate an extension to the BEAST2 package birth-death skyline model (BDSKY), BDSKY[Formula: see text], which introduces a scaling factor for the transmission rate between independent, jointly inferred trees. In an extensive simulation study, we show that BDSKY[Formula: see text] robustly infers the relative transmission rates under different epidemic scenarios. Using publicly available genome data of SARS-CoV-2, we apply BDSKY[Formula: see text] to quantify the transmission advantage of the Omicron over the Delta variant in Berlin, Germany. We find the overall transmission rate of Omicron to be scaled by a factor of two with pronounced variation between the individual clusters of each variant. These results quantify the transmission advantage of Omicron over the previously circulating Delta variant, in a crucial period of pre-established non-pharmaceutical interventions. By inferring variant- as well as cluster-specific transmission rate scaling factors, we show the differences in transmission dynamics for each variant. This highlights the importance of incorporating lineage-specific transmission differences in phylodynamic inference.
Collapse
Affiliation(s)
- Ariane Weber
- Transmission, Infection, Diversification & Evolution Group (tide), Max Planck Institute of Geoanthropology, Kahlaische Strasse 10, Jena, Thuringia 07745, Germany
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Saxony 04103, Germany
| | | | - Denise Kühnert
- Transmission, Infection, Diversification & Evolution Group (tide), Max Planck Institute of Geoanthropology, Kahlaische Strasse 10, Jena, Thuringia 07745, Germany
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Saxony 04103, Germany
- Centre for Artificial Intelligence in Public Health Research, Robert Koch Institute, Ludwig-Witthöft-Straße 14, Wildau, Brandenburg 15745, Germany
| |
Collapse
|
10
|
Judson SD, Munster VJ. The Multiple Origins of Ebola Disease Outbreaks. J Infect Dis 2023; 228:S465-S473. [PMID: 37592878 PMCID: PMC10651193 DOI: 10.1093/infdis/jiad352] [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: 03/22/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND The origins of Ebola disease outbreaks remain enigmatic. Historically outbreaks have been attributed to spillover events from wildlife. However, recent data suggest that some outbreaks may originate from human-to-human transmission of prior outbreak strains instead of spillover. Clarifying the origins of Ebola disease outbreaks could improve detection and mitigation of future outbreaks. METHODS We reviewed the origins of all Ebola disease outbreaks from 1976 to 2022 to analyze the earliest cases and characteristics of each outbreak. The epidemiology and phylogenetic relationships of outbreak strains were used to further identify the likely source of each outbreak. RESULTS From 1976 to 2022 there were 35 Ebola disease outbreaks with 48 primary/index cases. While the majority of outbreaks were associated with wildlife spillover, resurgence of human-to-human transmission could account for roughly a quarter of outbreaks caused by Ebola virus. Larger outbreaks were more likely to lead to possible resurgence, and nosocomial transmission was associated with the majority of outbreaks. CONCLUSIONS While spillover from wildlife has been a source for many Ebola disease outbreaks, multiple outbreaks may have originated from flare-ups of prior outbreak strains. Improving access to diagnostics as well as identifying groups at risk for resurgence of ebolaviruses will be crucial to preventing future outbreaks.
Collapse
Affiliation(s)
- Seth D Judson
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Vincent J Munster
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| |
Collapse
|
11
|
Wong W, Schaffner SF, Thwing J, Seck MC, Gomis J, Diedhiou Y, Sy N, Ndiop M, Ba F, Diallo I, Sene D, Diallo MA, Ndiaye YD, Sy M, Sene A, Sow D, Dieye B, Tine A, Ribado J, Suresh J, Lee A, Battle KE, Proctor JL, Bever CA, MacInnis B, Ndiaye D, Hartl DL, Wirth DF, Volkman SK. Evaluating the performance of Plasmodium falciparum genetics for inferring National Malaria Control Program reported incidence in Senegal. RESEARCH SQUARE 2023:rs.3.rs-3516287. [PMID: 37961451 PMCID: PMC10635402 DOI: 10.21203/rs.3.rs-3516287/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Genetic surveillance of the Plasmodium falciparum parasite shows great promise for helping National Malaria Control Programs (NMCPs) assess parasite transmission. Genetic metrics such as the frequency of polygenomic (multiple strain) infections, genetic clones, and the complexity of infection (COI, number of strains per infection) are correlated with transmission intensity. However, despite these correlations, it is unclear whether genetic metrics alone are sufficient to estimate clinical incidence. Here, we examined parasites from 3,147 clinical infections sampled between the years 2012-2020 through passive case detection (PCD) across 16 clinic sites spread throughout Senegal. Samples were genotyped with a 24 single nucleotide polymorphism (SNP) molecular barcode that detects parasite strains, distinguishes polygenomic (multiple strain) from monogenomic (single strain) infections, and identifies clonal infections. To determine whether genetic signals can predict incidence, we constructed a series of Poisson generalized linear mixed-effects models to predict the incidence level at each clinical site from a set of genetic metrics designed to measure parasite clonality, superinfection, and co-transmission rates. We compared the model-predicted incidence with the reported standard incidence data determined by the NMCP for each clinic and found that parasite genetic metrics generally correlated with reported incidence, with departures from expected values at very low annual incidence (<10/1000/annual [‰]). When transmission is greater than 10 cases per 1000 annual parasite incidence (annual incidence >10 ‰), parasite genetics can be used to accurately infer incidence and is consistent with superinfection-based hypotheses of malaria transmission. When transmission was <10 ‰, we found that many of the correlations between parasite genetics and incidence were reversed, which we hypothesize reflects the disproportionate impact of importation and focal transmission on parasite genetics when local transmission levels are low.
Collapse
Affiliation(s)
| | | | | | - Mame Cheikh Seck
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Jules Gomis
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Younouss Diedhiou
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Ngayo Sy
- Section de Lutte Anti-Parasitaire (SLAP) Clinic
| | | | - Fatou Ba
- Programme National de Lutte Contre le Paludisme
| | - Ibrahima Diallo
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Doudou Sene
- Programme National de Lutte Contre le Paludisme
| | - Mamadou Alpha Diallo
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Yaye Die Ndiaye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Mouhamad Sy
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Aita Sene
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Djiby Sow
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Baba Dieye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Abdoulaye Tine
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Jessica Ribado
- Institute for Disease Modeling, Bill and Melinda Gates Foundation
| | - Joshua Suresh
- Institute for Disease Modeling, Bill and Melinda Gates Foundation
| | - Albert Lee
- Institute for Disease Modeling, Bill and Melinda Gates Foundation
| | | | - Joshua L Proctor
- Institute for Disease Modeling, Bill and Melinda Gates Foundation
| | - Caitlin A Bever
- Institute for Disease Modeling, Bill and Melinda Gates Foundation
| | | | - Daouda Ndiaye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | | | | | | |
Collapse
|
12
|
Oh C, Zhou A, O'Brien K, Schmidt AR, Geltz J, Shisler JL, Schmidt AR, Keefer L, Brown WM, Nguyen TH. Improved performance of nucleic acid-based assays for genetically diverse norovirus surveillance. Appl Environ Microbiol 2023; 89:e0033123. [PMID: 37791775 PMCID: PMC10654041 DOI: 10.1128/aem.00331-23] [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: 02/24/2023] [Accepted: 07/07/2023] [Indexed: 10/05/2023] Open
Abstract
Nucleic acid-based assays, such as polymerase chain reaction (PCR), that amplify and detect organism-specific genome sequences are a standard method for infectious disease surveillance. However, challenges arise for virus surveillance because of their genetic diversity. Here, we calculated the variability of nucleotides within the genomes of 10 human viral species in silico and found that endemic viruses exhibit a high percentage of variable nucleotides (e.g., 51.4% for norovirus genogroup II). This genetic diversity led to the variable probability of detection of PCR assays (the proportion of viral sequences that contain the assay's target sequences divided by the total number of viral sequences). We then experimentally confirmed that the probability of the target sequence detection is indicative of the number of mismatches between PCR assays and norovirus genomes. Next, we developed a degenerate PCR assay that detects 97% of known norovirus genogroup II genome sequences and recognized norovirus in eight clinical samples. By contrast, previously developed assays with 31% and 16% probability of detection had 1.1 and 2.5 mismatches on average, respectively, which negatively impacted RNA quantification. In addition, the two PCR assays with a lower probability of detection also resulted in false negatives for wastewater-based epidemiology. Our findings suggest that the probability of detection serves as a simple metric for evaluating nucleic acid-based assays for genetically diverse virus surveillance.IMPORTANCENucleic acid-based assays, such as polymerase chain reaction (PCR), that amplify and detect organism-specific genome sequences are employed widely as a standard method for infectious disease surveillance. However, challenges arise for virus surveillance because of the rapid evolution and genetic variation of viruses. The study analyzed clinical and wastewater samples using multiple PCR assays and found significant performance variation among the PCR assays for genetically diverse norovirus surveillance. This finding suggests that some PCR assays may miss detecting certain virus strains, leading to a compromise in detection sensitivity. To address this issue, we propose a metric called the probability of detection, which can be simply calculated in silico using a code developed in this study, to evaluate nucleic acid-based assays for genetically diverse virus surveillance. This new approach can help improve the sensitivity and accuracy of virus detection, which is crucial for effective infectious disease surveillance and control.
Collapse
Affiliation(s)
- Chamteut Oh
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, Florida, USA
| | - Aijia Zhou
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Kate O'Brien
- School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Arthur R. Schmidt
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Joshua Geltz
- Division of Laboratories, Illinois Department of Public Health, Springfield, Illinois, USA
| | - Joanna L. Shisler
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Arthur R. Schmidt
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Laura Keefer
- Illinois State Water Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - William M. Brown
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Thanh H. Nguyen
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Institute of Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| |
Collapse
|
13
|
Ma W, Shi L, Li M. A fast and accurate method for SARS-CoV-2 genomic tracing. Brief Bioinform 2023; 24:bbad339. [PMID: 37779249 DOI: 10.1093/bib/bbad339] [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: 07/08/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 10/03/2023] Open
Abstract
To contain infectious diseases, it is crucial to determine the origin and transmission routes of the pathogen, as well as how the virus evolves. With the development of genome sequencing technology, genome epidemiology has emerged as a powerful approach for investigating the source and transmission of pathogens. In this study, we first presented the rationale for genomic tracing of SARS-CoV-2 and the challenges we currently face. Identifying the most genetically similar reference sequence to the query sequence is a critical step in genome tracing, typically achieved using either a phylogenetic tree or a sequence similarity search. However, these methods become inefficient or computationally prohibitive when dealing with tens of millions of sequences in the reference database, as we encountered during the COVID-19 pandemic. To address this challenge, we developed a novel genomic tracing algorithm capable of processing 6 million SARS-CoV-2 sequences in less than a minute. Instead of constructing a giant phylogenetic tree, we devised a weighted scoring system based on mutation characteristics to quantify sequences similarity. The developed method demonstrated superior performance compared to previous methods. Additionally, an online platform was developed to facilitate genomic tracing and visualization of the spatiotemporal distribution of sequences. The method will be a valuable addition to standard epidemiological investigations, enabling more efficient genomic tracing. Furthermore, the computational framework can be easily adapted to other pathogens, paving the way for routine genomic tracing of infectious diseases.
Collapse
Affiliation(s)
- Wentai Ma
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Leisheng Shi
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingkun Li
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
14
|
Mitchell J. Antimicrobial resistance (AMR) as a form of human-wildlife conflict: Why and how nondomesticated species should be incorporated into AMR guidance. Ecol Evol 2023; 13:e10421. [PMID: 37664497 PMCID: PMC10468991 DOI: 10.1002/ece3.10421] [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: 05/16/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
The challenge of antimicrobial resistance (AMR) continues to receive significant global attention as common infections become increasingly resistant to the drugs used to treat them. Once an infectious microbe has developed a mechanism of resistance, it can cause longer, more damaging infections which are more costly, time-consuming, and sometimes impossible to treat. Such impacts occur across the health of humans, animals, plants, and the environment. Thus, AMR is considered a One Health issue. However, current narratives on AMR focus on humans, food-producing animals, crops, and their immediate environments. Very little attention is given to wildlife in terms of the impact of AMR on their health, nor their role in the evolution and spread of AMR. This article (1) discusses an absence of wildlife in current AMR guidance, (2) suggests how this absence of wildlife could limit understanding of, and action on, AMR, (3) proposes that considering AMR as a form of human-wildlife conflict could enable AMR guidance to better incorporate wildlife into action planning and create a truly One Health approach to tackle AMR.
Collapse
Affiliation(s)
- Jessica Mitchell
- Nuffield Centre for International Health and Development, Leeds Institute for Health Sciences, Faculty of Medicine and HealthUniversity of LeedsLeedsUK
| |
Collapse
|
15
|
Malik S, Waheed Y. Tracing down the updates on Ebola virus surges: An update on anti-ebola therapeutic strategies. J Transl Int Med 2023; 11:216-225. [PMID: 37662888 PMCID: PMC10474883 DOI: 10.2478/jtim-2023-0100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023] Open
Abstract
Ebola virus (EBOV) related health complications have presented a great threat to the healthcare system in the endemic regions. The outbreaks of 2013-2016 and 2018-2020 brought along a huge healthcare burden for the afected communities. Knowing the seriousness of the matter, a series of research experiments have been actively carried out to devise efective therapeutics, drugs, and vaccination protocols against the Ebola virus disease (EVD) in the past decade. The purpose of this piece of literature is to shed light on vaccination protocols being clinically evaluated for EVD. A methodological approach has been adopted to gather relevant data from the latest publications. The compiled data include the molecular mechanistic insights into Ebola infection and a brief overview of diferent vaccination strategies: inactivated and DNA vaccines, virus-like particles and replicons, reverse genetic and recombinant approaches, entry, ion, and gene expression inhibitors, and some repurposed drugs. This data will help the scientific community to get a comprehensive overview of therapeutic interventions against Ebola that could be related to modifying EBOV vaccines and designing other antiviral vaccinations. Having said that, further work in modern therapeutic design is pertinent to tackle and lessen the healthcare burden expected from such outbreaks in the future.
Collapse
Affiliation(s)
- Shiza Malik
- Bridging Health Foundation, Rawalpindi, Punjab46000, Pakistan
| | - Yasir Waheed
- Office of Research, Innovation, and Commercialization (ORIC), Shaheed Zulfiqar Ali Bhutto Medical University (SZABMU), Islamabad44000, Pakistan
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos1401, Lebanon
| |
Collapse
|
16
|
Hepp B, Lorieux F, Degaugue A, Oberto J. VAPEX: an interactive web server for the deep exploration of natural virus and phage genomes. Bioinformatics 2023; 39:btad528. [PMID: 37624923 PMCID: PMC10471898 DOI: 10.1093/bioinformatics/btad528] [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: 05/11/2023] [Revised: 08/08/2023] [Accepted: 08/23/2023] [Indexed: 08/27/2023] Open
Abstract
MOTIVATION Studying the genetic makeup of viruses and phages through genome analysis is crucial for comprehending their function in causing diseases, progressing medicine, tracing their evolutionary history, monitoring the environment, and creating innovative biotechnologies. However, accessing the necessary data can be challenging due to a lack of dedicated comparative genomic tools and viral and phage databases, which are often outdated. Moreover, many wet bench experimentalists may not have the computational proficiency required to manipulate large amounts of genomic data. RESULTS We have developed VAPEX (Virus And Phage EXplorer), a web server which is supported by a database and features a user-friendly web interface. This tool enables users to easily perform various genomic analysis queries on all natural viruses and phages that have been fully sequenced and are listed in the NCBI compendium. VAPEX therefore excels in producing visual depictions of fully resolved synteny maps, which is one of its key strengths. VAPEX has the ability to exhibit a vast array of orthologous gene classes simultaneously through the use of symbolic representation. Additionally, VAPEX can fully analyze user-submitted viral and phage genomes, including those that have not yet been annotated. AVAILABILITY AND IMPLEMENTATION VAPEX can be accessed from all current web browsers such as Chrome, Firefox, Edge, Safari, and Opera. VAPEX is freely accessible at https://archaea.i2bc.paris-saclay.fr/vapex/.
Collapse
Affiliation(s)
- Benjamin Hepp
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris‐Saclay, 91198 Gif‐sur‐Yvette cedex, France
| | - Florence Lorieux
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris‐Saclay, 91198 Gif‐sur‐Yvette cedex, France
| | - Augustin Degaugue
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris‐Saclay, 91198 Gif‐sur‐Yvette cedex, France
| | - Jacques Oberto
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris‐Saclay, 91198 Gif‐sur‐Yvette cedex, France
| |
Collapse
|
17
|
Xu J, Xue Y, Bolinger AA, Li J, Zhou M, Chen H, Li H, Zhou J. Therapeutic potential of salicylamide derivatives for combating viral infections. Med Res Rev 2023; 43:897-931. [PMID: 36905090 PMCID: PMC10247541 DOI: 10.1002/med.21940] [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: 11/23/2021] [Revised: 11/09/2022] [Accepted: 02/26/2023] [Indexed: 03/12/2023]
Abstract
Since time immemorial human beings have constantly been fighting against viral infections. The ongoing and devastating coronavirus disease 2019 pandemic represents one of the most severe and most significant public health emergencies in human history, highlighting an urgent need to develop broad-spectrum antiviral agents. Salicylamide (2-hydroxybenzamide) derivatives, represented by niclosamide and nitazoxanide, inhibit the replication of a broad range of RNA and DNA viruses such as flavivirus, influenza A virus, and coronavirus. Moreover, nitazoxanide was effective in clinical trials against different viral infections including diarrhea caused by rotavirus and norovirus, uncomplicated influenza A and B, hepatitis B, and hepatitis C. In this review, we summarize the broad antiviral activities of salicylamide derivatives, the clinical progress, and the potential targets or mechanisms against different viral infections and highlight their therapeutic potential in combating the circulating and emerging viral infections in the future.
Collapse
Affiliation(s)
- Jimin Xu
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Yu Xue
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Andrew A. Bolinger
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Jun Li
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Mingxiang Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Haiying Chen
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Hongmin Li
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| |
Collapse
|
18
|
Ruivinho C, Gama-Carvalho M. Small non-coding RNAs encoded by RNA viruses: old controversies and new lessons from the COVID-19 pandemic. Front Genet 2023; 14:1216890. [PMID: 37415603 PMCID: PMC10322155 DOI: 10.3389/fgene.2023.1216890] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/07/2023] [Indexed: 07/08/2023] Open
Abstract
The recurring outbreaks caused by emerging RNA viruses have fostered an increased interest in the research of the mechanisms that regulate viral life cycles and the pathological outcomes associated with infections. Although interactions at the protein level are well-studied, interactions mediated by RNA molecules are less explored. RNA viruses can encode small non-coding RNAs molecules (sncRNAs), including viral miRNAs (v-miRNAs), that play important roles in modulating host immune responses and viral replication by targeting viral or host transcripts. Starting from the analysis of public databases compiling the known repertoire of viral ncRNA molecules and the evolution of publications and research interests on this topic in the wake of the COVID-19 pandemic, we provide an updated view on the current knowledge on viral sncRNAs, with a focus on v-miRNAs encoded by RNA viruses, and their mechanisms of action. We also discuss the potential of these molecules as diagnostic and prognostic biomarkers for viral infections and the development of antiviral therapies targeting v-miRNAs. This review emphasizes the importance of continued research efforts to characterize sncRNAs encoded by RNA viruses, identifies the most relevant pitfalls in the study of these molecules, and highlights the paradigm changes that have occurred in the last few years regarding their biogenesis, prevalence and functional relevance in the context of host-pathogen interactions.
Collapse
|
19
|
Zeghbib S, Kemenesi G, Jakab F. The importance of equally accessible genomic surveillance in the age of pandemics. Biol Futur 2023:10.1007/s42977-023-00164-5. [PMID: 37199870 DOI: 10.1007/s42977-023-00164-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [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.
Collapse
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
| |
Collapse
|
20
|
Guo X, Liu D, Huang Y, Deng Y, Wang Y, Mao J, Zhou Y, Xiong Y, Gao X. Revolutionizing viral disease vaccination: the promising clinical advancements of non-replicating mRNA vaccines. Virol J 2023; 20:64. [PMID: 37029389 PMCID: PMC10081822 DOI: 10.1186/s12985-023-02023-0] [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: 02/21/2023] [Accepted: 03/28/2023] [Indexed: 04/09/2023] Open
Abstract
The mRNA vaccine technology was developed rapidly during the global pandemic of COVID-19. The crucial role of the COVID-19 mRNA vaccine in preventing viral infection also have been beneficial to the exploration and application of other viral mRNA vaccines, especially for non-replication structure mRNA vaccines of viral disease with outstanding research results. Therefore, this review pays attention to the existing mRNA vaccines, which are of great value for candidates for clinical applications in viral diseases. We provide an overview of the optimization of the mRNA vaccine development process as well as the good immune efficacy and safety shown in clinical studies. In addition, we also provide a brief description of the important role of mRNA immunomodulators in the treatment of viral diseases. After that, it will provide a good reference or strategy for research on mRNA vaccines used in clinical medicine with more stable structures, higher translation efficiency, better immune efficacy and safety, shorter production time, and lower production costs than conditional vaccines to be used as preventive or therapeutic strategy for the control of viral diseases in the future.
Collapse
Affiliation(s)
- Xiao Guo
- School of Basic Medicine, Zunyi Medical University, West No. 6 Xuefu Road, Xinpu District, Zunyi, 563006, Guizhou, People's Republic of China
| | - Dongying Liu
- School of Basic Medicine, Zunyi Medical University, West No. 6 Xuefu Road, Xinpu District, Zunyi, 563006, Guizhou, People's Republic of China
| | - Yukai Huang
- School of Basic Medicine, Zunyi Medical University, West No. 6 Xuefu Road, Xinpu District, Zunyi, 563006, Guizhou, People's Republic of China
| | - Youcai Deng
- Department of Hematology, College of Pharmacy, Army Medical University (Third Military Medical University), Chongqing, People's Republic of China
| | - Ying Wang
- Modern Medical Teaching and Research Section, Department of Tibetan Medicine, University of Tibetan Medicine, No. 10 Dangre Middle Rd, Chengguan District, Lhasa, 850000, Tibet Autonomous Region, People's Republic of China
| | - Jingrui Mao
- School of Basic Medicine, Zunyi Medical University, West No. 6 Xuefu Road, Xinpu District, Zunyi, 563006, Guizhou, People's Republic of China
| | - Yuancheng Zhou
- Livestock and Poultry Biological Products Key Laboratory of Sichuan Province, Sichuan Animal Science Academy. No, 6 Niusha Road, Jinjiang District, Chengdu, 610299, People's Republic of China
| | - Yongai Xiong
- School of Pharmacy, Zunyi Medical University, West No. 6 Xuefu Road, Xinpu District, Zunyi, 563006, Guizhou, People's Republic of China.
| | - Xinghong Gao
- School of Basic Medicine, Zunyi Medical University, West No. 6 Xuefu Road, Xinpu District, Zunyi, 563006, Guizhou, People's Republic of China.
- Key Laboratory of Infectious Disease and Bio-Safety, Provincial Department of Education, Zunyi Medical University, West No. 6 Xuefu Road, Xinpu District, Zunyi, 563006, Guizhou, People's Republic of China.
| |
Collapse
|
21
|
Markov PV, Ghafari M, Beer M, Lythgoe K, Simmonds P, Stilianakis NI, Katzourakis A. The evolution of SARS-CoV-2. Nat Rev Microbiol 2023; 21:361-379. [PMID: 37020110 DOI: 10.1038/s41579-023-00878-2] [Citation(s) in RCA: 234] [Impact Index Per Article: 234.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2023] [Indexed: 04/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deaths and substantial morbidity worldwide. Intense scientific effort to understand the biology of SARS-CoV-2 has resulted in daunting numbers of genomic sequences. We witnessed evolutionary events that could mostly be inferred indirectly before, such as the emergence of variants with distinct phenotypes, for example transmissibility, severity and immune evasion. This Review explores the mechanisms that generate genetic variation in SARS-CoV-2, underlying the within-host and population-level processes that underpin these events. We examine the selective forces that likely drove the evolution of higher transmissibility and, in some cases, higher severity during the first year of the pandemic and the role of antigenic evolution during the second and third years, together with the implications of immune escape and reinfections, and the increasing evidence for and potential relevance of recombination. In order to understand how major lineages, such as variants of concern (VOCs), are generated, we contrast the evidence for the chronic infection model underlying the emergence of VOCs with the possibility of an animal reservoir playing a role in SARS-CoV-2 evolution, and conclude that the former is more likely. We evaluate uncertainties and outline scenarios for the possible future evolutionary trajectories of SARS-CoV-2.
Collapse
Affiliation(s)
- Peter V Markov
- European Commission, Joint Research Centre (JRC), Ispra, Italy.
- London School of Hygiene & Tropical Medicine, University of London, London, UK.
| | - Mahan Ghafari
- Big Data Institute, University of Oxford, Oxford, UK
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Insel Riems, Germany
| | | | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nikolaos I Stilianakis
- European Commission, Joint Research Centre (JRC), Ispra, Italy
- Department of Biometry and Epidemiology, University of Erlangen-Nuremberg, Erlangen, Germany
| | | |
Collapse
|
22
|
Sun B, Ni M, Liu H, Liu D. Viral intra-host evolutionary dynamics revealed via serial passage of Japanese encephalitis virus in vitro. Virus Evol 2023; 9:veac103. [PMID: 37205166 PMCID: PMC10185921 DOI: 10.1093/ve/veac103] [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: 04/26/2022] [Revised: 10/04/2022] [Accepted: 03/21/2023] [Indexed: 12/02/2023] Open
Abstract
Analyses of viral inter- and intra-host mutations could better guide the prevention and control of infectious diseases. For a long time, studies on viral evolution have focused on viral inter-host variations. Next-generation sequencing has accelerated the investigations of viral intra-host diversity. However, the theoretical basis and dynamic characteristics of viral intra-host mutations remain unknown. Here, using serial passages of the SA14-14-2 vaccine strain of Japanese encephalitis virus (JEV) as the in vitro model, the distribution characteristics of 1,788 detected intra-host single-nucleotide variations (iSNVs) and their mutated frequencies from 477 deep-sequenced samples were analyzed. Our results revealed that in adaptive (baby hamster kidney (BHK)) cells, JEV is under a nearly neutral selection pressure, and both non-synonymous and synonymous mutations represent an S-shaped growth trend over time. A higher positive selection pressure was observed in the nonadaptive (C6/36) cells, and logarithmic growth in non-synonymous iSNVs and linear growth in synonymous iSNVs were observed over time. Moreover, the mutation rates of the NS4B protein and the untranslated region (UTR) of the JEV are significantly different between BHK and C6/36 cells, suggesting that viral selection pressure is regulated by different cellular environments. In addition, no significant difference was detected in the distribution of mutated frequencies of iSNVs between BHK and C6/36 cells.
Collapse
Affiliation(s)
- Bangyao Sun
- School of Medical Laboratory, Weifang Medical University, Baotong West Street, Weifang 261053, China
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Xiaohongshan 44#, Wuhan 430000, China
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Xiaohongshan 44#, Wuhan 430000, China
- University of Chinese Academy of Sciences, Yuquan Road 19#, Beijing 100049, China
| | - Ming Ni
- Beijing Institute of Radiation Medicine, Taiping Road 27#, Beijing 100850, China
| | - Haizhou Liu
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Xiaohongshan 44#, Wuhan 430000, China
| | - Di Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Xiaohongshan 44#, Wuhan 430000, China
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Xiaohongshan 44#, Wuhan 430000, China
- University of Chinese Academy of Sciences, Yuquan Road 19#, Beijing 100049, China
| |
Collapse
|
23
|
Ibba R, Corona P, Nonne F, Caria P, Serreli G, Palmas V, Riu F, Sestito S, Nieddu M, Loddo R, Sanna G, Piras S, Carta A. Design, Synthesis, and Antiviral Activities of New Benzotriazole-Based Derivatives. Pharmaceuticals (Basel) 2023; 16:ph16030429. [PMID: 36986528 PMCID: PMC10054465 DOI: 10.3390/ph16030429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 03/16/2023] Open
Abstract
Several human diseases are caused by enteroviruses and are currently clinically untreatable, pushing the research to identify new antivirals. A notable number of benzo[d][1,2,3]triazol-1(2)-yl derivatives were designed, synthesized, and in vitro evaluated for cytotoxicity and antiviral activity against a wide spectrum of RNA positive- and negative-sense viruses. Five of them (11b, 18e, 41a, 43a, 99b) emerged for their selective antiviral activity against Coxsackievirus B5, a human enteroviruses member among the Picornaviridae family. The EC50 values ranged between 6 and 18.5 μM. Among all derivatives, compounds 18e and 43a were interestingly active against CVB5 and were selected to better define the safety profile on cell monolayers by transepithelial resistance test (TEER). Results indicated compound 18e as the hit compound to investigate the potential mechanism of action by apoptosis assay, virucidal activity test, and the time of addition assay. CVB5 is known to be cytotoxic by inducing apoptosis in infected cells; in this study, compound 18e was proved to protect cells from viral infection. Notably, cells were mostly protected when pre-treated with derivative 18e, which had, however, no virucidal activity. From the performed biological assays, compound 18e turned out to be non-cytotoxic as well as cell protective against CVB5 infection, with a mechanism of action ascribable to an interaction on the early phase of infection, by hijacking the viral attachment process.
Collapse
Affiliation(s)
- Roberta Ibba
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Via Muroni, 23/A, 07100 Sassari, Italy; (R.I.); (P.C.); (F.R.); (M.N.)
| | - Paola Corona
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Via Muroni, 23/A, 07100 Sassari, Italy; (R.I.); (P.C.); (F.R.); (M.N.)
| | - Francesca Nonne
- GSK Vaccine Institute for Global Health GSK, Via Fiorentina, 1, 53100 Siena, Italy;
| | - Paola Caria
- Department of Biomedical Sciences, Section of Microbiology and Virology, University of Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy; (P.C.); (G.S.); (V.P.); (R.L.)
| | - Gabriele Serreli
- Department of Biomedical Sciences, Section of Microbiology and Virology, University of Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy; (P.C.); (G.S.); (V.P.); (R.L.)
| | - Vanessa Palmas
- Department of Biomedical Sciences, Section of Microbiology and Virology, University of Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy; (P.C.); (G.S.); (V.P.); (R.L.)
| | - Federico Riu
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Via Muroni, 23/A, 07100 Sassari, Italy; (R.I.); (P.C.); (F.R.); (M.N.)
- Department of Chemistry, Biomedicinskt Centrum, BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Simona Sestito
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, Via Vienna 2, 07100 Sassari, Italy;
| | - Maria Nieddu
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Via Muroni, 23/A, 07100 Sassari, Italy; (R.I.); (P.C.); (F.R.); (M.N.)
| | - Roberta Loddo
- Department of Biomedical Sciences, Section of Microbiology and Virology, University of Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy; (P.C.); (G.S.); (V.P.); (R.L.)
| | - Giuseppina Sanna
- Department of Biomedical Sciences, Section of Microbiology and Virology, University of Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy; (P.C.); (G.S.); (V.P.); (R.L.)
- Correspondence: (G.S.); (S.P.)
| | - Sandra Piras
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Via Muroni, 23/A, 07100 Sassari, Italy; (R.I.); (P.C.); (F.R.); (M.N.)
- Correspondence: (G.S.); (S.P.)
| | - Antonio Carta
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Via Muroni, 23/A, 07100 Sassari, Italy; (R.I.); (P.C.); (F.R.); (M.N.)
| |
Collapse
|
24
|
Khandelwal V, Sharma T, Gupta S, Singh S, Sharma MK, Parashar D, Kashyap VK. Stem cell therapy: a novel approach against emerging and re-emerging viral infections with special reference to SARS-CoV-2. Mol Biol Rep 2023; 50:2663-2683. [PMID: 36536185 PMCID: PMC9762873 DOI: 10.1007/s11033-022-07957-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 09/17/2022] [Indexed: 12/23/2022]
Abstract
The past several decades have witnessed the emergence and re-emergence of many infectious viral agents, flaviviruses, influenza, filoviruses, alphaviruses, and coronaviruses since the advent of human deficiency virus (HIV). Some of them even become serious threats to public health and have raised major global health concerns. Several different medicinal compounds such as anti-viral, anti-malarial, and anti-inflammatory agents, are under investigation for the treatment of these viral diseases. These therapies are effective improving recovery rates and overall survival of patients but are unable to heal lung damage caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Therefore, there is a critical need to identify effective treatments to combat this unmet clinical need. Due to its antioxidant and immunomodulatory properties, stem cell therapy is considered a novel approach to regenerate damaged lungs and reduce inflammation. Stem cell therapy uses a heterogeneous subset of regenerative cells that can be harvested from various adult tissue types and is gaining popularity due to its prodigious regenerative potential as well as immunomodulatory and anti-inflammatory properties. These cells retain expression of cluster of differentiation markers (CD markers), interferon-stimulated gene (ISG), reduce expression of pro-inflammatory cytokines and, show a rapid proliferation rate, which makes them an attractive tool for cellular therapies and to treat various inflammatory and viral-induced injuries. By examining various clinical studies, this review demonstrates positive considerations for the implications of stem cell therapy and presents a necessary approach for treating virally induced infections in patients.
Collapse
Affiliation(s)
- Vishal Khandelwal
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, 281406, India
| | - Tarubala Sharma
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, 281406, India
| | - Saurabh Gupta
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, 281406, India
| | - Shoorvir Singh
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, 281406, India
| | - Manish Kumar Sharma
- Department of Microbiology, Dr. Ram Manohar Lohia Avadh University, Faizabad, Uttar Pradesh, 224001, India
| | - Deepak Parashar
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
| | - Vivek K Kashyap
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX, 78504, USA. .,South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX, 78504, USA.
| |
Collapse
|
25
|
A case for investment in clinical metagenomics in low-income and middle-income countries. THE LANCET. MICROBE 2023; 4:e192-e199. [PMID: 36563703 DOI: 10.1016/s2666-5247(22)00328-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 12/24/2022]
Abstract
Clinical metagenomics is the diagnostic approach with the broadest capacity to detect both known and novel pathogens. Clinical metagenomics is costly to run and requires infrastructure, but the use of next-generation sequencing for SARS-CoV-2 molecular epidemiology in low-income and middle-income countries (LMICs) offers an opportunity to direct this infrastructure to the establishment of clinical metagenomics programmes. Local implementation of clinical metagenomics is important to create relevant systems and evaluate cost-effective methodologies for its use, as well as to ensure that reference databases and result interpretation tools are appropriate to local epidemiology. Rational implementation, based on the needs of LMICs and the available resources, could ultimately improve individual patient care in instances in which available diagnostics are inadequate and supplement emerging infectious disease surveillance systems to ensure the next pandemic pathogen is quickly identified.
Collapse
|
26
|
Krishnan SK, Nataraj N, Meyyappan M, Pal U. Graphene-Based Field-Effect Transistors in Biosensing and Neural Interfacing Applications: Recent Advances and Prospects. Anal Chem 2023; 95:2590-2622. [PMID: 36693046 DOI: 10.1021/acs.analchem.2c03399] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Siva Kumar Krishnan
- CONACYT-Instituto de Física, Benemérita Universidad Autónoma de Puebla, Apdo. Postal J-48, Puebla72570, Mexico
| | - Nandini Nataraj
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, No.1, Section 3, Chung-Hsiao East Road, Taipei106, Taiwan
| | - M Meyyappan
- Centre for Nanotechnology, Indian Institute of Technology, Guwahati781039, Assam, India
| | - Umapada Pal
- Instituto de Física, Benemérita Universidad Autónoma de Puebla, Apdo. Postal J-48, Puebla72570, Mexico
| |
Collapse
|
27
|
Gruber MF, Rubin S, Krause PR. Approaches to demonstrating the effectiveness of filovirus vaccines: Lessons from Ebola and COVID-19. Front Immunol 2023; 14:1109486. [PMID: 36817425 PMCID: PMC9932497 DOI: 10.3389/fimmu.2023.1109486] [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: 11/27/2022] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
Zaire ebolavirus (EBOV), Sudan ebolavirus (SUDV) and Marburg virus (MARV), are members of the Filoviridae family that can cause severe disease and death in humans and animals. The reemergence of Ebola, Sudan and Marburg virus disease highlight the need for continued availability of safe and effectives vaccines as well as development of new vaccines. While randomized controlled trials using disease endpoints provide the most robust assessment of vaccine effectiveness, challenges to this approach include the unpredictable size, location, occurrence and duration of filovirus disease outbreaks. Thus, other approaches to demonstrating vaccine effectiveness have been considered. These approaches are discussed using examples of preventive vaccines against other infectious diseases. In addition, this article proposes a clinical immunobridging strategy using licensed EBOV vaccines as comparators for demonstrating the effectiveness of filovirus vaccine candidates that are based on the same licensed vaccine platform technology.
Collapse
Affiliation(s)
- Marion F. Gruber
- International AIDS Vaccine Initiative, New York, NY, United States,*Correspondence: Marion F. Gruber,
| | - Steven Rubin
- GlaxoSmithKline (GSk), Rockville, MD, United States
| | | |
Collapse
|
28
|
Rai A, Hamiidah N, Abbass M, Masunga DS, Shoumar H, Kantawala BI, Wellington J, Uwishema O. Ebola Virus Disease in Uganda: A global emergency call. Ann Med Surg (Lond) 2022; 84:104825. [DOI: 10.1016/j.amsu.2022.104825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/30/2022] [Indexed: 11/09/2022] Open
|
29
|
Yu X, Cheng G. Contribution of phylogenetics to understanding the evolution and epidemiology of dengue virus. Animal Model Exp Med 2022; 5:410-417. [PMID: 36245335 PMCID: PMC9610151 DOI: 10.1002/ame2.12283] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/05/2022] [Indexed: 11/18/2022] Open
Abstract
Dengue virus (DENV) is one of the most important arboviral pathogens in the tropics and subtropics, and nearly one‐third of the world's population is at risk of infection. The transmission of DENV involves a sylvatic cycle between nonhuman primates (NHP) and Aedes genus mosquitoes, and an endemic cycle between human hosts and predominantly Aedes aegypti. DENV belongs to the genus Flavivirus of the family Flaviviridae and consists of four antigenically distinct serotypes (DENV‐1‐4). Phylogenetic analyses of DENV have revealed its origin, epidemiology, and the drivers that determine its molecular evolution in nature. This review discusses how phylogenetic research has improved our understanding of DENV evolution and how it affects viral ecology and improved our ability to analyze and predict future DENV emergence.
Collapse
Affiliation(s)
- Xi Yu
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China.,Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, China.,Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Gong Cheng
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China.,Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, China.,Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| |
Collapse
|
30
|
Oral Rabies Vaccine Strain SPBN GASGAS: Genetic Stability after Serial In Vitro and In Vivo Passaging. Viruses 2022; 14:v14102136. [PMID: 36298691 PMCID: PMC9609770 DOI: 10.3390/v14102136] [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: 07/27/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
Oral vaccination of wildlife has shown to be a very effective management tool in rabies control. Evaluation of the genetic stability of vaccine viruses before distributing vaccine baits in the environment is essential because all available oral rabies vaccines, including the genetically engineered rabies virus vaccine strain SPBN GASGAS (Rabitec), are based on replication-competent viruses. To evaluate the genetic stability of this vaccine strain, five serial passages of the Master Seed Virus (MSV) in the production cell line BHK21 Cl13 were performed. Furthermore, to test possible reversion to virulence, a back-passage study in suckling mouse brain (SMB) was performed. Subsequently, the pooled 5th SMB passage was inoculated intracerebrally (i.c.) in adult and suckling mice. The full genome sequences of the isolated 5th passage, in vivo and in vitro, were compared at both the consensus and the quasispecies level with the MSV. Additionally, the full genome sequence of the 6th SMB passage from the individual animals was determined and compared. Full-length integration of the double glycoprotein and modified base substitutions at amino acid position 194 and 333 of the glycoprotein could be verified in all 5th and 6th passage samples. Overall, 11 single nucleotide polymorphisms (SNPs) were detected in the 5th pooled SMB passage, 4 with frequency between 10 and 20%, and 7 with between 2.5 and 10%. SNPs that resulted in amino acid exchange were found in genes: N (one SNP), G (four SNPs), and L (three SNPs). However, none of these SNPs were associated with reversion to virulence since all adult mice inoculated i.c. with this material survived. In the individual samples of the 6th SMB passage 24 additional SNPs (>2.5%) were found, of which only 1 SNP (L-gene, position 6969) had a prevalence of >50% in 3 of 17 samples. The obtained results confirmed the stable expression of genetic modifications and the genetic stability of the consensus strain after serial in vivo and in vitro passaging.
Collapse
|
31
|
Lin M, Chen H, Jia L, Yang M, Qiu S, Song H, Wang L, Zheng T. Using a grey relational analysis in an improved Grunow-Finke assessment tool to detect unnatural epidemics. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2022; 43:1508-1517. [PMID: 36100578 DOI: 10.1111/risa.14016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The Grunow-Finke epidemiological assessment tool (GFT) has several limitations in its ability to differentiate between natural and man-made epidemics. Our study aimed to improve the GFT and analyze historical epidemics to validate the model. Using a gray relational analysis (GRA), we improved the GFT by revising the existing standards and adding five new standards. We then removed the artificial weights and final decision threshold. Finally, by using typically unnatural epidemic events as references, we used the GRA to calculate the unnatural probability and obtain assessment results. Using the advanced tool, we conducted retrospective and case analyses to test its performance. In the validation set of 13 historical epidemics, unnatural and natural epidemics were divided into two categories near the unnatural probability of 45%, showing evident differences (p < 0.01) and an assessment accuracy close to 100%. The unnatural probabilities of the Ebola virus disease of 2013 and Middle East Respiratory Syndrome of 2012 were 30.6% and 36.1%, respectively. Our advanced epidemic assessment tool improved the accuracy of the original GFT from approximately 55% to approximately 100% and reduced the impact of human factors on these outcomes effectively.
Collapse
Affiliation(s)
- Mengxuan Lin
- Academy of Military Medical Sciences, Academy of Military Science of Chinese PLA, Beijing, China
| | - Hui Chen
- Department of Infectious Disease Prevention and Control, Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | - Leili Jia
- Department of Infectious Disease Prevention and Control, Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | - Mingjuan Yang
- Department of Infectious Disease Prevention and Control, Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | - Shaofu Qiu
- Department of Infectious Disease Prevention and Control, Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | - Hongbin Song
- Department of Infectious Disease Prevention and Control, Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | - Ligui Wang
- Department of Infectious Disease Prevention and Control, Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | - Tao Zheng
- Academy of Military Medical Sciences, Academy of Military Science of Chinese PLA, Beijing, China
| |
Collapse
|
32
|
Wong W, Volkman S, Daniels R, Schaffner S, Sy M, Ndiaye YD, Badiane AS, Deme AB, Diallo MA, Gomis J, Sy N, Ndiaye D, Wirth DF, Hartl DL. R H: a genetic metric for measuring intrahost Plasmodium falciparum relatedness and distinguishing cotransmission from superinfection. PNAS NEXUS 2022; 1:pgac187. [PMID: 36246152 PMCID: PMC9552330 DOI: 10.1093/pnasnexus/pgac187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 09/08/2022] [Indexed: 01/29/2023]
Abstract
Multiple-strain (polygenomic) infections are a ubiquitous feature of Plasmodium falciparum parasite population genetics. Under simple assumptions of superinfection, polygenomic infections are hypothesized to be the result of multiple infectious bites. As a result, polygenomic infections have been used as evidence of repeat exposure and used to derive genetic metrics associated with high transmission intensity. However, not all polygenomic infections are the result of multiple infectious bites. Some result from the transmission of multiple, genetically related strains during a single infectious bite (cotransmission). Superinfection and cotransmission represent two distinct transmission processes, and distinguishing between the two could improve inferences regarding parasite transmission intensity. Here, we describe a new metric, R H, that utilizes the correlation in allelic state (heterozygosity) within polygenomic infections to estimate the likelihood that the observed complexity resulted from either superinfection or cotransmission. R H is flexible and can be applied to any type of genetic data. As a proof of concept, we used R H to quantify polygenomic relatedness and estimate cotransmission and superinfection rates from a set of 1,758 malaria infections genotyped with a 24 single nucleotide polymorphism (SNP) molecular barcode. Contrary to expectation, we found that cotransmission was responsible for a significant fraction of 43% to 53% of the polygenomic infections collected in three distinct epidemiological regions in Senegal. The prediction that polygenomic infections frequently result from cotransmission stresses the need to incorporate estimates of relatedness within polygenomic infections to ensure the accuracy of genomic epidemiology surveillance data for informing public health activities.
Collapse
Affiliation(s)
- Wesley Wong
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 665 Huntington Ave, Boston, MA 02115, USA
| | - Sarah Volkman
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 665 Huntington Ave, Boston, MA 02115, USA
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
- College of Natural, Behavioral, and Health Sciences, Simmons University, Boston, MA 02115, USA
| | - Rachel Daniels
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 665 Huntington Ave, Boston, MA 02115, USA
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Stephen Schaffner
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Mouhamad Sy
- Laboratory of Parasitology and Mycology, Aristide le Dantec Hospital, Cheikh Anta Diop University, Dakar 10200, Senegal
| | - Yaye Die Ndiaye
- Laboratory of Parasitology and Mycology, Aristide le Dantec Hospital, Cheikh Anta Diop University, Dakar 10200, Senegal
| | - Aida S Badiane
- Laboratory of Parasitology and Mycology, Aristide le Dantec Hospital, Cheikh Anta Diop University, Dakar 10200, Senegal
| | - Awa B Deme
- Laboratory of Parasitology and Mycology, Aristide le Dantec Hospital, Cheikh Anta Diop University, Dakar 10200, Senegal
| | - Mamadou Alpha Diallo
- Laboratory of Parasitology and Mycology, Aristide le Dantec Hospital, Cheikh Anta Diop University, Dakar 10200, Senegal
| | - Jules Gomis
- Laboratory of Parasitology and Mycology, Aristide le Dantec Hospital, Cheikh Anta Diop University, Dakar 10200, Senegal
| | - Ngayo Sy
- Laboratory of Parasitology and Mycology, Aristide le Dantec Hospital, Cheikh Anta Diop University, Dakar 10200, Senegal
| | - Daouda Ndiaye
- Laboratory of Parasitology and Mycology, Aristide le Dantec Hospital, Cheikh Anta Diop University, Dakar 10200, Senegal
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 665 Huntington Ave, Boston, MA 02115, USA
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| |
Collapse
|
33
|
Grimaldi A, Panariello F, Annunziata P, Giuliano T, Daniele M, Pierri B, Colantuono C, Salvi M, Bouché V, Manfredi A, Cuomo MC, Di Concilio D, Tiberio C, Fiorenza M, Portella G, Cimmino I, Sorrentino A, Fusco G, Granata MR, Cerino P, Limone A, Atripaldi L, Ballabio A, Cacchiarelli D. Improved SARS-CoV-2 sequencing surveillance allows the identification of new variants and signatures in infected patients. Genome Med 2022; 14:90. [PMID: 35962405 PMCID: PMC9372932 DOI: 10.1186/s13073-022-01098-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/29/2022] [Indexed: 12/12/2022] Open
Abstract
Background Genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the only approach to rapidly monitor and tackle emerging variants of concern (VOC) of the COVID-19 pandemic. Such scrutiny is crucial to limit the spread of VOC that might escape the immune protection conferred by vaccination strategies or previous virus exposure. It is also becoming clear now that efficient genomic surveillance would require monitoring of the host gene expression to identify prognostic biomarkers of treatment efficacy and disease progression. Here we propose an integrative workflow to both generate thousands of SARS-CoV-2 genome sequences per week and analyze host gene expression upon infection. Methods In this study we applied an integrated workflow for RNA extracted from nasal swabs to obtain in parallel the full genome of SARS-CoV-2 and transcriptome of host respiratory epithelium. The RNA extracted from each sample was reverse transcribed and the viral genome was specifically enriched through an amplicon-based approach. The very same RNA was then used for patient transcriptome analysis. Samples were collected in the Campania region, Italy, for viral genome sequencing. Patient transcriptome analysis was performed on about 700 samples divided into two cohorts of patients, depending on the viral variant detected (B.1 or delta). Results We sequenced over 20,000 viral genomes since the beginning of the pandemic, producing the highest number of sequences in Italy. We thus reconstructed the pandemic dynamics in the regional territory from March 2020 to December 2021. In addition, we have matured and applied novel proof-of-principle approaches to prioritize possible gain-of-function mutations by leveraging patients’ metadata and isolated patient-specific signatures of SARS-CoV-2 infection. This allowed us to (i) identify three new viral variants that specifically originated in the Campania region, (ii) map SARS-CoV-2 intrahost variability during long-term infections and in one case identify an increase in the number of mutations in the viral genome, and (iii) identify host gene expression signatures correlated with viral load in upper respiratory ways. Conclusion In conclusion, we have successfully generated an optimized and cost-effective strategy to monitor SARS-CoV-2 genetic variability, without the need of automation. Thus, our approach is suitable for any lab with a benchtop sequencer and a limited budget, allowing an integrated genomic surveillance on premises. Finally, we have also identified a gene expression signature defining SARS-CoV-2 infection in real-world patients’ upper respiratory ways. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01098-8.
Collapse
Affiliation(s)
- Antonio Grimaldi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Francesco Panariello
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Patrizia Annunziata
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.,Next Generation Diagnostic srl, Pozzuoli, Italy
| | - Teresa Giuliano
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Michela Daniele
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.,Next Generation Diagnostic srl, Pozzuoli, Italy
| | - Biancamaria Pierri
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo. Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Chiara Colantuono
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.,Next Generation Diagnostic srl, Pozzuoli, Italy
| | - Marcello Salvi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.,Next Generation Diagnostic srl, Pozzuoli, Italy
| | - Valentina Bouché
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Anna Manfredi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.,Next Generation Diagnostic srl, Pozzuoli, Italy
| | - Maria Concetta Cuomo
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo. Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Denise Di Concilio
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo. Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Claudia Tiberio
- UOC Microbiologia e Virologia, P.O. Cotugno A.O. dei Colli, Naples, Italy
| | - Mariano Fiorenza
- Department of Translational Medicine, University of Naples Federico II, Naples, Italy
| | - Giuseppe Portella
- Department of Translational Medicine, University of Naples Federico II, Naples, Italy
| | - Ilaria Cimmino
- Department of Translational Medicine, University of Naples Federico II, Naples, Italy.,UOC Epidemiologia e Prevenzione, ASL Napoli 2 Nord, Dipartimento di Prevenzione, Casavatore, Italy
| | - Antonio Sorrentino
- UOC Epidemiologia e Prevenzione, ASL Napoli 2 Nord, Dipartimento di Prevenzione, Casavatore, Italy
| | - Giovanna Fusco
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo. Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Maria Rosaria Granata
- UOC Epidemiologia e Prevenzione, ASL Napoli 2 Nord, Dipartimento di Prevenzione, Casavatore, Italy
| | - Pellegrino Cerino
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo. Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Antonio Limone
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo. Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Luigi Atripaldi
- UOC Microbiologia e Virologia, P.O. Cotugno A.O. dei Colli, Naples, Italy
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.,Department of Translational Medicine, University of Naples Federico II, Naples, Italy.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, USA.,SSM School for Advanced Studies, University of Naples Federico II, Naples, Italy
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy. .,Department of Translational Medicine, University of Naples Federico II, Naples, Italy. .,SSM School for Advanced Studies, University of Naples Federico II, Naples, Italy.
| |
Collapse
|
34
|
Tiemessen MM, Solforosi L, Dekking L, Czapska-Casey D, Serroyen J, Sullivan NJ, Volkmann A, Pau MG, Callendret B, Schuitemaker H, Luhn K, Zahn R, Roozendaal R. Protection against Marburg Virus and Sudan Virus in NHP by an Adenovector-Based Trivalent Vaccine Regimen Is Correlated to Humoral Immune Response Levels. Vaccines (Basel) 2022; 10:1263. [PMID: 36016151 PMCID: PMC9412258 DOI: 10.3390/vaccines10081263] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/21/2022] [Accepted: 08/01/2022] [Indexed: 11/20/2022] Open
Abstract
The Marburg virus (MARV) and Sudan virus (SUDV) belong to the filovirus family. The sporadic human outbreaks occur mostly in Africa and are characterized by an aggressive disease course with high mortality. The first case of Marburg virus disease in Guinea in 2021, together with the increased frequency of outbreaks of Ebola virus (EBOV), which is also a filovirus, accelerated the interest in potential prophylactic vaccine solutions against multiple filoviruses. We previously tested a two-dose heterologous vaccine regimen (Ad26.Filo, MVA-BN-Filo) in non-human primates (NHP) and showed a fully protective immune response against both SUDV and MARV in addition to the already-reported protective effect against EBOV. The vaccine-induced glycoprotein (GP)-binding antibody levels appear to be good predictors of the NHP challenge outcome as indicated by the correlation between antibody levels and survival outcome as well as the high discriminatory capacity of the logistic model. Moreover, the elicited GP-specific binding antibody response against EBOV, SUDV, and MARV remains stable for more than 1 year. Overall, the NHP data indicate that the Ad26.Filo, MVA-BN-Filo regimen may be a good candidate for a prophylactic vaccination strategy in regions at high risk of filovirus outbreaks.
Collapse
Affiliation(s)
- Machteld M. Tiemessen
- Janssen Vaccines & Prevention B.V., Archimedesweg 6, 2333 CN Leiden, The Netherlands
| | - Laura Solforosi
- Janssen Vaccines & Prevention B.V., Archimedesweg 6, 2333 CN Leiden, The Netherlands
| | - Liesbeth Dekking
- Janssen Vaccines & Prevention B.V., Archimedesweg 6, 2333 CN Leiden, The Netherlands
| | | | - Jan Serroyen
- Janssen Vaccines & Prevention B.V., Archimedesweg 6, 2333 CN Leiden, The Netherlands
| | - Nancy J. Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ariane Volkmann
- Bavarian Nordic GmbH, Fraunhoferstrasse 13, D-82152 Martinsried, Germany
| | - Maria Grazia Pau
- Janssen Vaccines & Prevention B.V., Archimedesweg 6, 2333 CN Leiden, The Netherlands
| | - Benoit Callendret
- Janssen Vaccines & Prevention B.V., Archimedesweg 6, 2333 CN Leiden, The Netherlands
| | - Hanneke Schuitemaker
- Janssen Vaccines & Prevention B.V., Archimedesweg 6, 2333 CN Leiden, The Netherlands
| | - Kerstin Luhn
- Janssen Vaccines & Prevention B.V., Archimedesweg 6, 2333 CN Leiden, The Netherlands
| | - Roland Zahn
- Janssen Vaccines & Prevention B.V., Archimedesweg 6, 2333 CN Leiden, The Netherlands
| | - Ramon Roozendaal
- Janssen Vaccines & Prevention B.V., Archimedesweg 6, 2333 CN Leiden, The Netherlands
| |
Collapse
|
35
|
Balloux F, Tan C, Swadling L, Richard D, Jenner C, Maini M, van Dorp L. The past, current and future epidemiological dynamic of SARS-CoV-2. OXFORD OPEN IMMUNOLOGY 2022; 3:iqac003. [PMID: 35872966 PMCID: PMC9278178 DOI: 10.1093/oxfimm/iqac003] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/11/2022] [Accepted: 06/15/2022] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2, the agent of the COVID-19 pandemic, emerged in late 2019 in China, and rapidly spread throughout the world to reach all continents. As the virus expanded in its novel human host, viral lineages diversified through the accumulation of around two mutations a month on average. Different viral lineages have replaced each other since the start of the pandemic, with the most successful Alpha, Delta and Omicron variants of concern (VoCs) sequentially sweeping through the world to reach high global prevalence. Neither Alpha nor Delta was characterized by strong immune escape, with their success coming mainly from their higher transmissibility. Omicron is far more prone to immune evasion and spread primarily due to its increased ability to (re-)infect hosts with prior immunity. As host immunity reaches high levels globally through vaccination and prior infection, the epidemic is expected to transition from a pandemic regime to an endemic one where seasonality and waning host immunization are anticipated to become the primary forces shaping future SARS-CoV-2 lineage dynamics. In this review, we consider a body of evidence on the origins, host tropism, epidemiology, genomic and immunogenetic evolution of SARS-CoV-2 including an assessment of other coronaviruses infecting humans. Considering what is known so far, we conclude by delineating scenarios for the future dynamic of SARS-CoV-2, ranging from the good-circulation of a fifth endemic 'common cold' coronavirus of potentially low virulence, the bad-a situation roughly comparable with seasonal flu, and the ugly-extensive diversification into serotypes with long-term high-level endemicity.
Collapse
Affiliation(s)
- François Balloux
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Cedric Tan
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 138672 Singapore, Singapore
| | - Leo Swadling
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Damien Richard
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Charlotte Jenner
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Mala Maini
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| |
Collapse
|
36
|
Xiao M, Tian F, Liu X, Zhou Q, Pan J, Luo Z, Yang M, Yi C. Virus Detection: From State-of-the-Art Laboratories to Smartphone-Based Point-of-Care Testing. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105904. [PMID: 35393791 PMCID: PMC9110880 DOI: 10.1002/advs.202105904] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/27/2022] [Indexed: 05/07/2023]
Abstract
Infectious virus outbreaks pose a significant challenge to public healthcare systems. Early and accurate virus diagnosis is critical to prevent the spread of the virus, especially when no specific vaccine or effective medicine is available. In clinics, the most commonly used viral detection methods are molecular techniques that involve the measurement of nucleic acids or proteins biomarkers. However, most clinic-based methods require complex infrastructure and expensive equipment, which are not suitable for low-resource settings. Over the past years, smartphone-based point-of-care testing (POCT) has rapidly emerged as a potential alternative to laboratory-based clinical diagnosis. This review summarizes the latest development of virus detection. First, laboratory-based and POCT-based viral diagnostic techniques are compared, both of which rely on immunosensing and nucleic acid detection. Then, various smartphone-based POCT diagnostic techniques, including optical biosensors, electrochemical biosensors, and other types of biosensors are discussed. Moreover, this review covers the development of smartphone-based POCT diagnostics for various viruses including COVID-19, Ebola, influenza, Zika, HIV, et al. Finally, the prospects and challenges of smartphone-based POCT diagnostics are discussed. It is believed that this review will aid researchers better understand the current challenges and prospects for achieving the ultimate goal of containing disease-causing viruses worldwide.
Collapse
Affiliation(s)
- Meng Xiao
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical EngineeringShenzhen Campus of Sun Yat‐Sen UniversityShenzhen518107P. R. China
| | - Feng Tian
- Department of Biomedical EngineeringThe Hong Kong Polytechnic UniversityHunghomHong Kong999077P. R. China
| | - Xin Liu
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical EngineeringShenzhen Campus of Sun Yat‐Sen UniversityShenzhen518107P. R. China
| | - Qiaoqiao Zhou
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical EngineeringShenzhen Campus of Sun Yat‐Sen UniversityShenzhen518107P. R. China
| | - Jiangfei Pan
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical EngineeringShenzhen Campus of Sun Yat‐Sen UniversityShenzhen518107P. R. China
| | - Zhaofan Luo
- Department of Clinical LaboratoryThe Seventh Affiliated Hospital of Sun Yat‐Sen UniversityShenzhen518107P. R. China
| | - Mo Yang
- Department of Biomedical EngineeringThe Hong Kong Polytechnic UniversityHunghomHong Kong999077P. R. China
| | - Changqing Yi
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical EngineeringShenzhen Campus of Sun Yat‐Sen UniversityShenzhen518107P. R. China
| |
Collapse
|
37
|
Sonnleitner ST, Prelog M, Sonnleitner S, Hinterbichler E, Halbfurter H, Kopecky DBC, Almanzar G, Koblmüller S, Sturmbauer C, Feist L, Horres R, Posch W, Walder G. Cumulative SARS-CoV-2 mutations and corresponding changes in immunity in an immunocompromised patient indicate viral evolution within the host. Nat Commun 2022; 13:2560. [PMID: 35538074 PMCID: PMC9090742 DOI: 10.1038/s41467-022-30163-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 04/19/2022] [Indexed: 01/07/2023] Open
Abstract
Different scenarios explaining the emergence of novel variants of concern (VOC) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been reported, including their evolution in scarcely monitored populations, in animals as alternative hosts, or in immunocompromised individuals. Here we report SARS-CoV-2 immune escape mutations over a period of seven months in an immunocompromised patient with prolonged viral shedding. Signs of infection, viral shedding and mutation events are periodically analyzed using RT-PCR and next-generation sequencing based on naso-pharyngeal swabs, with the results complemented by immunological diagnostics to determine humoral and T cell immune responses. Throughout the infection course, 17 non-synonymous intra-host mutations are noted, with 15 (88.2%) having been previously described as prominent immune escape mutations (S:E484K, S:D950N, S:P681H, S:N501Y, S:del(9), N:S235F and S:H655Y) in VOCs. The high frequency of these non-synonymous mutations is consistent with multiple events of convergent evolution. Thus, our results suggest that specific mutations in the SARS-CoV-2 genome may represent positions with a fitness advantage, and may serve as targets in future vaccine and therapeutics development for COVID-19. Variants of concerns arise from SARS-CoV-2 mutations poise as severe public health threats. Here the authors chronicle SARS-CoV-2 mutations onset and immune parameters in an immunocompromised patient with continuous virus-shedding, thereby hinting potential intra-host viral evolution and escape facilitated by ineffective T cell immunity.
Collapse
Affiliation(s)
- Sissy Therese Sonnleitner
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria. .,Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020, Innsbruck, Austria.
| | - Martina Prelog
- Pediatric Rheumatology/Special Immunology, Department of Pediatrics, University Hospital Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, Germany
| | - Stefanie Sonnleitner
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria
| | - Eva Hinterbichler
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria
| | - Hannah Halbfurter
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria
| | - Dominik B C Kopecky
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria
| | - Giovanni Almanzar
- Pediatric Rheumatology/Special Immunology, Department of Pediatrics, University Hospital Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, Germany
| | - Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Christian Sturmbauer
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Leonard Feist
- GenXPro GmbH, Altenhoeferallee 3, 60438, Frankfurt am Main, Germany
| | - Ralf Horres
- GenXPro GmbH, Altenhoeferallee 3, 60438, Frankfurt am Main, Germany
| | - Wilfried Posch
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Gernot Walder
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria
| |
Collapse
|
38
|
Smirnova I, Petrova A, Lobov A, Minnibaeva E, Phoung TTT, Van LT, Khine MM, Esaulkova I, Slita A, Zarubaev V, Kazakova O. Azepanodipterocarpol is potential candidate for inhibits influenza H1N1 type among other lupane, oleanane, and dammarane A-ring amino-triterpenoids. J Antibiot (Tokyo) 2022; 75:258-267. [PMID: 35246615 PMCID: PMC8894567 DOI: 10.1038/s41429-022-00514-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 11/26/2022]
Abstract
A series of lupane-, oleanane- and dammarane-based triterpenoids with 3β-amino, A-ring azepano- and 3,4-seco-fragments has been synthesized and evaluated for antiviral activity against influenza A(H1N1) virus. It was found that azepanodipterocarpol 8 and 3β-amino-28-oxoallobetulin 11 showed antiviral activity with IC50 1.1 and 2.6 μg ml-1, and selectivity index of 19 and 10, respectively.
Collapse
Affiliation(s)
- Irina Smirnova
- Ufa Institute of Chemistry, Ufa Federal Research Center, Russian Academy of Sciences, 71 pr. Oktyabrya, 450054, Ufa, Russian Federation.
| | - Anastasiya Petrova
- Ufa Institute of Chemistry, Ufa Federal Research Center, Russian Academy of Sciences, 71 pr. Oktyabrya, 450054, Ufa, Russian Federation
| | - Alexander Lobov
- Ufa Institute of Chemistry, Ufa Federal Research Center, Russian Academy of Sciences, 71 pr. Oktyabrya, 450054, Ufa, Russian Federation
| | - El'za Minnibaeva
- Department of Technical Chemistry and Materials Science, Bashkir State University, Faculty of Engineering, 32 Zaki Validi, 450076, Ufa, Russian Federation
| | - Thao Tran Thi Phoung
- Institute of Chemistry - Vietnamese Academy of Science and Technology 18, Hoang Quoc Viet street 18 Cau Giay district, Hanoi, Vietnam
| | - Loc Tran Van
- Institute of Chemistry - Vietnamese Academy of Science and Technology 18, Hoang Quoc Viet street 18 Cau Giay district, Hanoi, Vietnam
| | - Myint Myint Khine
- Department of Chemistry, University of Yangon, University Avenue Road, Kamayut Township, 11041, Yangon, Myanmar
| | - Iana Esaulkova
- Department of virology, St. Petersburg Pasteur Institute of Epidemiology and Microbiology, Experimental virology laboratory, 14 Mira St., St. Petersburg, 197001, Russian Federation
| | - Alexander Slita
- Department of virology, St. Petersburg Pasteur Institute of Epidemiology and Microbiology, Experimental virology laboratory, 14 Mira St., St. Petersburg, 197001, Russian Federation
| | - Vladimir Zarubaev
- Department of virology, St. Petersburg Pasteur Institute of Epidemiology and Microbiology, Experimental virology laboratory, 14 Mira St., St. Petersburg, 197001, Russian Federation
| | - Oxana Kazakova
- Ufa Institute of Chemistry, Ufa Federal Research Center, Russian Academy of Sciences, 71 pr. Oktyabrya, 450054, Ufa, Russian Federation
| |
Collapse
|
39
|
Qiu Q, Yang C, Wang Y, Alexander CA, Yi G, Zhang Y, Qin X, Yang YY. Silane-functionalized polyionenes-coated cotton fabrics with potent antimicrobial and antiviral activities. Biomaterials 2022; 284:121470. [DOI: 10.1016/j.biomaterials.2022.121470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/16/2022] [Accepted: 03/12/2022] [Indexed: 12/26/2022]
|
40
|
Abstract
6 years ago, I published a Cell Host and Microbe paper that described randomization of virus genetic populations during mosquito infection. From within the evolutionary chaos, however, there is an order that can reveal a virus' past. Using these insights, I forged a career harnessing virus evolution to understand epidemiological patterns.
Collapse
|
41
|
Repurposing drugs targeting epidemic viruses. Drug Discov Today 2022; 27:1874-1894. [DOI: 10.1016/j.drudis.2022.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/01/2022] [Accepted: 04/07/2022] [Indexed: 02/06/2023]
|
42
|
Huo S, Hai Y, Guo Y, Nie L, Li H, Qiao P, Zong K, Li X, Guo Y, Song J, Zhao H, Lei W, Lan Y, Liu WJ, Gao GF. Intra-host variation and evolutionary dynamics of adenoviruses correlate to neutrophils in infected patients. J Med Virol 2022; 94:3863-3875. [PMID: 35355288 DOI: 10.1002/jmv.27744] [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: 01/08/2022] [Revised: 03/26/2022] [Accepted: 03/30/2022] [Indexed: 11/10/2022]
Abstract
With deep sequencing of virus genomes within the hosts, intra-host single nucleotide variations (iSNVs) have been used for analyses of virus genome variation and evolution, which is indicated to correlate with viral pathogenesis and disease severity. Little is known about the features of iSNVs among DNA viruses. We performed the epidemiological and laboratory investigation of one outbreak of adenovirus. The whole genomes of viruses in both original oral swabs and cell-cultured virus isolates were deeply sequenced. We identified 737 iSNVs in the viral genomes sequenced from original samples and 46 viral iSNVs in cell cultured isolates, with 33 iSNVs shared by original samples and cultured isolates. Meanwhile, we found these 33 iSNVs were shared by different patients, among which, three hot-spot areas 6367-6401, 9213-9247 and 10584-10606 within the functional genes of the adenovirus genome were found. Notably, the substitution rates of iSNVs were closely correlated with the clinical and immune indicators of the patients. Especially a positive correlation to neutrophils was found, indicating a predictable biomarker of iSNV dynamics. Our findings demonstrated the neutrophil-correlated dynamic evolution features of the iSNVs within adenoviruses, which indicates a virus-host interaction during human infection of a DNA virus. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Shuting Huo
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.,NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China
| | - Yan Hai
- Inner Mongolia Center for Disease Control and Prevention, Hohhot, 010031, China
| | - Yaxin Guo
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China
| | - Li Nie
- Tongliao Center for Disease Control and Prevention, Tongliao, 028000, China
| | - Hongmei Li
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.,NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China
| | - Peiwen Qiao
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China
| | - Kexin Zong
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.,NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China
| | - Xin Li
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.,NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China
| | - Yuanyuan Guo
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China.,School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, China
| | - Jingdong Song
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China
| | - Honglan Zhao
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China
| | - Wenwen Lei
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China
| | - Yu Lan
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China
| | - William J Liu
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.,NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China
| | - George F Gao
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.,NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China.,CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| |
Collapse
|
43
|
De Benedictis P, Leopardi S, Markotter W, Velasco-Villa A. The Importance of Accurate Host Species Identification in the Framework of Rabies Surveillance, Control and Elimination. Viruses 2022; 14:v14030492. [PMID: 35336899 PMCID: PMC8954416 DOI: 10.3390/v14030492] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/31/2022] [Accepted: 02/23/2022] [Indexed: 02/03/2023] Open
Abstract
Accurate host identification is paramount to understand disease epidemiology and to apply appropriate control measures. This is especially important for multi-host pathogens such as the rabies virus, a major and almost invariably fatal zoonosis that has mobilized unanimous engagement at an international level towards the final goal of zero human deaths due to canine rabies. Currently, diagnostic laboratories implement a standardized identification using taxonomic keys. However, this method is challenged by high and undiscovered biodiversity, decomposition of carcasses and subjective misevaluation, as has been attested to by findings from a cohort of 242 archived specimens collected across Sub-Saharan Africa and submitted for rabies diagnosis. We applied two simple and cheap methods targeting the Cytochrome b and Cytochrome c oxidase subunit I to confirm the initial classification. We therefore suggest prioritizing a standardized protocol that includes, as a first step, the implementation of taxonomic keys at a family or subfamily level, followed by the molecular characterization of the host species.
Collapse
Affiliation(s)
- Paola De Benedictis
- FAO Reference Center for Rabies, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy;
- Correspondence:
| | - Stefania Leopardi
- FAO Reference Center for Rabies, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy;
| | - Wanda Markotter
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa;
| | - Andres Velasco-Villa
- Centers for Diseases Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30333, USA;
| |
Collapse
|
44
|
Bhowmik R, Manaithiya A, Vyas B, Nath R, Rehman S, Roy S, Roy R. Identification of potential inhibitor against Ebola virus VP35: insight into virtual screening, pharmacoinformatics profiling, and molecular dynamic studies. Struct Chem 2022. [DOI: 10.1007/s11224-022-01899-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
45
|
Liu Y, Sun B, Wang J, Sun H, Lu Z, Chen L, Lan M, Xu J, Pan J, Shi J, Sun Y, Zhang X, Wang J, Jiang D, Yang K. In silico analyses and experimental validation of the MHC class-I restricted epitopes of Ebolavirus GP. Int Immunol 2022; 34:313-325. [PMID: 35192720 DOI: 10.1093/intimm/dxac006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
Ebolavirus (EBOV) causes an extremely high mortality and prevalence disease called Ebola virus disease (EVD). There is only one glycoprotein (GP) on the virus particle surface, which mediates entry into the host cell. MHC class-I restricted CD8 + T cell responses are important antiviral immune responses. Therefore, it is of great importance to understand EBOV GP-specific MHC class-I restricted epitopes within immunogenicity. In this study, computational approaches were employed to predict the dominant MHC class-I molecule epitopes of EBOV GP for mouse H2 and major alleles of HLA class-I supertypes. Our results yielded 42 dominant epitopes in H2 haplotypes and 301 dominant epitopes in HLA class-I haplotypes. After validation by ELISpot assay, in-depth analyses to ascertain their nature of conservation, immunogenicity, and docking with the corresponding MHC class-I molecules were undertaken. Our study predicted MHC class-I restricted epitopes that may aid the advancement of anti-EBOV immune responses. And the integrated strategy of epitope prediction, validation, and comparative analyses were postulated, promising for epitope-based immunotherapy development and application to viral epidemics.
Collapse
Affiliation(s)
- Yang Liu
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China.,Shaanxi Provincial Center for Disease Control and Prevention, Xi'an, Shaanxi, P.R. China
| | - Baozeng Sun
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Jiawei Wang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Hao Sun
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China.,Tangshan Sannvhe Airport, Tangshan, Hebei, P.R. China
| | - Zhenhua Lu
- Department of Epidemiology, Public Health School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Longyu Chen
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Mingfu Lan
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Jiahao Xu
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Jingyu Pan
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Jingqi Shi
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Yuanjie Sun
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Xiyang Zhang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Jing Wang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Dongbo Jiang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Kun Yang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| |
Collapse
|
46
|
Tiper I, Kourout M, Lanning B, Fisher C, Konduru K, Purkayastha A, Kaplan G, Duncan R. Tracking ebolavirus genomic drift with a resequencing microarray. PLoS One 2022; 17:e0263732. [PMID: 35143574 PMCID: PMC8830711 DOI: 10.1371/journal.pone.0263732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 01/25/2022] [Indexed: 11/17/2022] Open
Abstract
Filoviruses are emerging pathogens that cause acute fever with high fatality rate and present a global public health threat. During the 2013–2016 Ebola virus outbreak, genome sequencing allowed the study of virus evolution, mutations affecting pathogenicity and infectivity, and tracing the viral spread. In 2018, early sequence identification of the Ebolavirus as EBOV in the Democratic Republic of the Congo supported the use of an Ebola virus vaccine. However, field-deployable sequencing methods are needed to enable a rapid public health response. Resequencing microarrays (RMA) are a targeted method to obtain genomic sequence on clinical specimens rapidly, and sensitively, overcoming the need for extensive bioinformatic analysis. This study presents the design and initial evaluation of an ebolavirus resequencing microarray (Ebolavirus-RMA) system for sequencing the major genomic regions of four Ebolaviruses that cause disease in humans. The design of the Ebolavirus-RMA system is described and evaluated by sequencing repository samples of three Ebolaviruses and two EBOV variants. The ability of the system to identify genetic drift in a replicating virus was achieved by sequencing the ebolavirus glycoprotein gene in a recombinant virus cultured under pressure from a neutralizing antibody. Comparison of the Ebolavirus-RMA results to the Genbank database sequence file with the accession number given for the source RNA and Ebolavirus-RMA results compared to Next Generation Sequence results of the same RNA samples showed up to 99% agreement.
Collapse
Affiliation(s)
- Irina Tiper
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | - Moussa Kourout
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | - Bryan Lanning
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | - Carolyn Fisher
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | - Krishnamurthy Konduru
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | | | - Gerardo Kaplan
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | - Robert Duncan
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
- * E-mail:
| |
Collapse
|
47
|
Ghafari M, du Plessis L, Raghwani J, Bhatt S, Xu B, Pybus OG, Katzourakis A. Purifying Selection Determines the Short-Term Time Dependency of Evolutionary Rates in SARS-CoV-2 and pH1N1 Influenza. Mol Biol Evol 2022; 39:6509523. [PMID: 35038728 PMCID: PMC8826518 DOI: 10.1093/molbev/msac009] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
High-throughput sequencing enables rapid genome sequencing during infectious disease outbreaks and provides an opportunity to quantify the evolutionary dynamics of pathogens in near real-time. One difficulty of undertaking evolutionary analyses over short timescales is the dependency of the inferred evolutionary parameters on the timespan of observation. Crucially, there are an increasing number of molecular clock analyses using external evolutionary rate priors to infer evolutionary parameters. However, it is not clear which rate prior is appropriate for a given time window of observation due to the time-dependent nature of evolutionary rate estimates. Here, we characterize the molecular evolutionary dynamics of SARS-CoV-2 and 2009 pandemic H1N1 (pH1N1) influenza during the first 12 months of their respective pandemics. We use Bayesian phylogenetic methods to estimate the dates of emergence, evolutionary rates, and growth rates of SARS-CoV-2 and pH1N1 over time and investigate how varying sampling window and data set sizes affect the accuracy of parameter estimation. We further use a generalized McDonald-Kreitman test to estimate the number of segregating nonneutral sites over time. We find that the inferred evolutionary parameters for both pandemics are time dependent, and that the inferred rates of SARS-CoV-2 and pH1N1 decline by ∼50% and ∼100%, respectively, over the course of 1 year. After at least 4 months since the start of sequence sampling, inferred growth rates and emergence dates remain relatively stable and can be inferred reliably using a logistic growth coalescent model. We show that the time dependency of the mean substitution rate is due to elevated substitution rates at terminal branches which are 2-4 times higher than those of internal branches for both viruses. The elevated rate at terminal branches is strongly correlated with an increasing number of segregating nonneutral sites, demonstrating the role of purifying selection in generating the time dependency of evolutionary parameters during pandemics.
Collapse
Affiliation(s)
- Mahan Ghafari
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Louis du Plessis
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Jayna Raghwani
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, United Kingdom
| | - Bo Xu
- Department of Earth System Science, Tsinghua University, Beijing, China
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
48
|
Diakou KI, Mitsis T, Pierouli K, Papakonstantinou E, Bongcam-Rudloff E, Wayengera M, Vlachakis D. Ebola Virus Disease and Current Therapeutic Strategies: A Review. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1339:131-137. [PMID: 35023100 DOI: 10.1007/978-3-030-78787-5_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The Ebola virus disease is a severe hemorrhagic fever that affects humans and other primates. Ebola virus, the causative agent of the disease, is transmitted to humans from wild animals and is highly contagious and aggressive with an estimated fatality rate to be around 50%. Since 1976, 11 outbreaks of Ebola virus disease have been reported in total, affecting mostly sub-Saharan Africa, while the most recent ongoing outbreak in the Democratic Republic of the Congo has more than 3000 reported cases and 72 deaths. Although an effective vaccine against Ebola virus disease has become available, no targeted treatment with proven efficacy upon infection is developed. Herein, we review the epidemiology of Ebola virus and the current situation in terms of prevention, diagnosis, and treatment of the disease.
Collapse
Affiliation(s)
- Kalliopi Io Diakou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Thanasis Mitsis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Katerina Pierouli
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Eleni Papakonstantinou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Erik Bongcam-Rudloff
- SLU-Global Bioinformatics Centre, Department of Animal Breeding and Genetics Science, University of Agricultural Sciences, Uppsala, Sweden
| | - Misaki Wayengera
- Department of Pathology, Unit of Genetics & Genomics, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Dimitrios Vlachakis
- DarkDNA Group, Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece. .,Lab of Molecular Endocrinology, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece. .,Department of Informatics, Faculty of Natural and Mathematical Sciences, King's College London, Strand, London, UK.
| |
Collapse
|
49
|
Li J, Du P, Yang L, Zhang J, Song C, Chen D, Song Y, Ding N, Hua M, Han K, Song R, Xie W, Chen Z, Wang X, Liu J, Xu Y, Gao G, Wang Q, Pu L, Di L, Li J, Yue J, Han J, Zhao X, Yan Y, Yu F, Wu AR, Zhang F, Gao YQ, Huang Y, Wang J, Zeng H, Chen C. Two-step fitness selection for intra-host variations in SARS-CoV-2. Cell Rep 2022; 38:110205. [PMID: 34982968 PMCID: PMC8674508 DOI: 10.1016/j.celrep.2021.110205] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/10/2021] [Accepted: 12/13/2021] [Indexed: 12/30/2022] Open
Abstract
Spontaneous mutations introduce uncertainty into coronavirus disease 2019 (COVID-19) control procedures and vaccine development. Here, we perform a spatiotemporal analysis on intra-host single-nucleotide variants (iSNVs) in 402 clinical samples from 170 affected individuals, which reveals an increase in genetic diversity over time after symptom onset in individuals. Nonsynonymous mutations are overrepresented in the pool of iSNVs but underrepresented at the single-nucleotide polymorphism (SNP) level, suggesting a two-step fitness selection process: a large number of nonsynonymous substitutions are generated in the host (positive selection), and these substitutions tend to be unfixed as SNPs in the population (negative selection). Dynamic iSNV changes in subpopulations with different gender, age, illness severity, and viral shedding time displayed a varied fitness selection process among populations. Our study highlights that iSNVs provide a mutational pool shaping the rapid global evolution of the virus.
Collapse
Affiliation(s)
- Jiarui Li
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China
| | - Pengcheng Du
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China
| | - Lijiang Yang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics, Biomedical Pioneering Innovation Center, Peking University, Beijing 100871, China
| | - Ju Zhang
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China
| | - Chuan Song
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China
| | - Danying Chen
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China
| | - Yangzi Song
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China
| | - Nan Ding
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China
| | - Mingxi Hua
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China
| | - Kai Han
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China
| | - Rui Song
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China
| | - Wen Xie
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China
| | - Zhihai Chen
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China
| | - Xianbo Wang
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China
| | - Jingyuan Liu
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China
| | - Yanli Xu
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China
| | - Guiju Gao
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China
| | - Qi Wang
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China
| | - Lin Pu
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China
| | - Lin Di
- Beijing Advanced Innovation Center for Genomics, Biomedical Pioneering Innovation Center, Peking University, Beijing 100871, China; School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Jie Li
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Jinglin Yue
- Peking University Ditan Teaching Hospital, Beijing 100015, China
| | - Junyan Han
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China
| | - Xuesen Zhao
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China
| | - Yonghong Yan
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China
| | - Fengting Yu
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China
| | - Angela R Wu
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, P.R. China; Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong SAR, P.R. China
| | - Fujie Zhang
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China.
| | - Yi Qin Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics, Biomedical Pioneering Innovation Center, Peking University, Beijing 100871, China; Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China.
| | - Yanyi Huang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics, Biomedical Pioneering Innovation Center, Peking University, Beijing 100871, China; School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518055, China; Chinese Institute for Brain Research, Beijing 102206, China.
| | - Jianbin Wang
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China; Chinese Institute for Brain Research, Beijing 102206, China.
| | - Hui Zeng
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China.
| | - Chen Chen
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China.
| |
Collapse
|
50
|
Chen Y, Li S, Wu W, Geng S, Mao M. Distinct mutations and lineages of SARS-CoV-2 virus in the early phase of COVID-19 pandemic and subsequent 1-year global expansion. J Med Virol 2022; 94:2035-2049. [PMID: 35001392 PMCID: PMC9015543 DOI: 10.1002/jmv.27580] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/28/2021] [Accepted: 01/06/2022] [Indexed: 12/14/2022]
Abstract
A novel coronavirus, SARS-CoV-2, has caused over 274 million cases and over 5.3 million deaths worldwide since it occurred in December 2019 in Wuhan, China. Here we conceptualized the temporospatial evolutionary and expansion dynamics of SARS-CoV-2 by taking a series of the cross-sectional view of viral genomes from early outbreak in January 2020 in Wuhan to the early phase of global ignition in early April, and finally to the subsequent global expansion by late December 2020. Based on the phylogenetic analysis of the early patients in Wuhan, Wuhan/WH04/2020 is supposed to be a more appropriate reference genome of SARS-CoV-2, instead of the first sequenced genome Wuhan-Hu-1. By scrutinizing the cases from the very early outbreak, we found a viral genotype from the Seafood Market in Wuhan featured with two concurrent mutations (i.e., M type) had become the overwhelmingly dominant genotype (95.3%) of the pandemic 1 year later. By analyzing 4013 SARS-CoV-2 genomes from different continents by early April, we were able to interrogate the viral genomic composition dynamics of the initial phase of global ignition over a time span of 14 weeks. Eleven major viral genotypes with unique geographic distributions were also identified. WE1 type, a descendant of M and predominantly witnessed in western Europe, consisted of half of all the cases (50.2%) at the time. The mutations of major genotypes at the same hierarchical level were mutually exclusive, which implies that various genotypes bearing the specific mutations were propagated during human-to-human transmission, not by accumulating hot-spot mutations during the replication of individual viral genomes. As the pandemic was unfolding, we also used the same approach to analyze 261 323 SARS-CoV-2 genomes from the world since the outbreak in Wuhan (i.e., including all the publicly available viral genomes) to recapitulate our findings over 1-year time span. By December 25, 2020, 95.3% of global cases were M type and 93.0% of M-type cases were WE1. In fact, at present all the five variants of concern (VOC) are the descendants of WE1 type. This study demonstrates that viral genotypes can be utilized as molecular barcodes in combination with epidemiologic data to monitor the spreading routes of the pandemic and evaluate the effectiveness of control measures. Moreover, the dynamics of viral mutational spectrum in the study may help the early identification of new strains in patients to reduce further spread of infection, guide the development of molecular diagnosis and vaccines against COVID-19, and help assess their accuracy and efficacy in real world at real time.
Collapse
Affiliation(s)
- Yan Chen
- Research & Development, SeekIn Inc., Shenzhen, China
| | - Shiyong Li
- Research & Development, SeekIn Inc., Shenzhen, China
| | - Wei Wu
- Research & Development, SeekIn Inc., Shenzhen, China
| | | | - Mao Mao
- Research & Development, SeekIn Inc., Shenzhen, China.,Yonsei Song-Dang Institute for Cancer Research, Yonsei University, Seoul, Korea
| |
Collapse
|