1
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Jia F, Shi Y, Yu Y. Structural homology-based identification of BEN domain proteins in Poxviruses. Biochem Biophys Res Commun 2024; 712-713:149933. [PMID: 38640730 DOI: 10.1016/j.bbrc.2024.149933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024]
Abstract
BEND family transcription factors directly interact with DNA through BEN domains and have been found across metazoan species. Interestingly, certain insect and mammalian viruses have also hijacked Bend genes into their genome. However, the phylogenetic classification and evolution of these viral BEN domains remain unclear. Building on our previous finding that in silico method accurately determine the 3D model of BEN domains, we used AlphaFold2 to predict the tertiary structures of poxviral BEN domains for comprehensive homologous comparison. We revealed that the majority of poxviral BEN modules exhibit characteristics of type II BEN. Additionally, electrostatic surface potential analysis found various poxviral BEN domains, including the first BEN of OPG067 in Orthopoxvirus, the third BEN of OPG067 in Yatapoxvirus and the third BEN of MC036R in MCV, have positively charged protein surfaces, indicating a structural basis for DNA loading. Notably, MC036R shares structural resemblance with human BEND3, as they both contain four BEN domains and an intrinsically disordered region. In summary, our discoveries provide deeper insights into the functional roles of BEN proteins within poxviruses.
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Affiliation(s)
- Fuchuan Jia
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
| | - Yixing Shi
- Chinese Institute for Brain Research, Beijing, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 102206, China
| | - Yang Yu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China.
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2
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I SB, E Z, A Č, A DL. Mpox virus DNA detection in different clinical specimens: tertiary-level laboratory experience, Bosnia and Herzegovina, 2022. Diagn Microbiol Infect Dis 2024; 109:116268. [PMID: 38513559 DOI: 10.1016/j.diagmicrobio.2024.116268] [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: 10/30/2023] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 03/23/2024]
Abstract
Mpox virus (MPXV) infection is difficult to distinguish from other (non-)infectious diseases. The etiology of rash can be differentiated by real-time polymerase chain reaction (rtPCR) on different types of samples. The study aims to provide experience with emerging MPXV diagnostics in a tertiary-level laboratory in Bosnia and Herzegovina. From July-December 2022, a total of 18 mpox suspected persons were tested. MPXV infection was confirmed by rtPCR in 10/18 (55.56 %) persons. The number of cases reached a peak in October 2022. The lowest median Crossing point (Cp) (x̄ = 29.76) was obtained from a swab of skin lesions in a viral transport medium (VTM). Evaluating the Cp values for the 7/9 mpox cases from whom paired swab samples from different anatomic sites were collected, higher positivity of skin lesion swabs in VTM was observed. In conclusion, our data highlighted the confirmatory role of rtPCR in the diagnosis of MPXV in skin lesion samples.
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Affiliation(s)
- Salimović-Bešić I
- Clinical Center of the University of Sarajevo, Unit for Clinical Microbiology, Bolnička 25, 71000 Sarajevo, Bosnia and Herzegovina; University of Sarajevo, Faculty of Health Studies, Stjepana Tomića 1, 71000 Sarajevo, Bosnia and Herzegovina.
| | - Zahirović E
- Clinical Center of the University of Sarajevo, Unit for Clinical Microbiology, Bolnička 25, 71000 Sarajevo, Bosnia and Herzegovina; University of Sarajevo, Faculty of Health Studies, Stjepana Tomića 1, 71000 Sarajevo, Bosnia and Herzegovina
| | - Čamdžić A
- Clinical Center of the University of Sarajevo, Unit for Clinical Microbiology, Bolnička 25, 71000 Sarajevo, Bosnia and Herzegovina
| | - Dedeić-Ljubović A
- Clinical Center of the University of Sarajevo, Unit for Clinical Microbiology, Bolnička 25, 71000 Sarajevo, Bosnia and Herzegovina; University of Sarajevo, Faculty of Health Studies, Stjepana Tomića 1, 71000 Sarajevo, Bosnia and Herzegovina; Sarajevo Medical School, University Sarajevo School of Science and Technology, Hrasnička cesta 3a, 71000 Sarajevo, Bosnia and Herzegovina
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3
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Moss B. Understanding the biology of monkeypox virus to prevent future outbreaks. Nat Microbiol 2024; 9:1408-1416. [PMID: 38724757 DOI: 10.1038/s41564-024-01690-1] [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: 05/15/2023] [Accepted: 03/26/2024] [Indexed: 06/07/2024]
Abstract
Historically, monkeypox (mpox) was a zoonotic disease endemic in Africa. However, in 2022, a global outbreak occurred following a substantial increase in cases in Africa, coupled with spread by international travellers to other continents. Between January 2022 and October 2023, about 91,000 confirmed cases from 115 countries were reported, leading the World Health Organization to declare a public health emergency. The basic biology of monkeypox virus (MPXV) can be inferred from other poxviruses, such as vaccinia virus, and confirmed by genome sequencing. Here the biology of MPXV is reviewed, together with a discussion of adaptive changes during MPXV evolution and implications for transmission. Studying MPXV biology is important to inform specific host interactions, to aid in ongoing outbreaks and to predict those in the future.
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Affiliation(s)
- Bernard Moss
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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4
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Suraweera CD, Espinoza B, Hinds MG, Kvansakul M. Mastering Death: The Roles of Viral Bcl-2 in dsDNA Viruses. Viruses 2024; 16:879. [PMID: 38932171 PMCID: PMC11209288 DOI: 10.3390/v16060879] [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: 05/07/2024] [Revised: 05/25/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Proteins of the Bcl-2 family regulate cellular fate via multiple mechanisms including apoptosis, autophagy, senescence, metabolism, inflammation, redox homeostasis, and calcium flux. There are several regulated cell death (RCD) pathways, including apoptosis and autophagy, that use distinct molecular mechanisms to elicit the death response. However, the same proteins/genes may be deployed in multiple biochemical pathways. In apoptosis, Bcl-2 proteins control the integrity of the mitochondrial outer membrane (MOM) by regulating the formation of pores in the MOM and apoptotic cell death. A number of prosurvival genes populate the genomes of viruses including those of the pro-survival Bcl-2 family. Viral Bcl-2 proteins are sequence and structural homologs of their cellular counterparts and interact with cellular proteins in apoptotic and autophagic pathways, potentially allowing them to modulate these pathways and determine cellular fate.
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Affiliation(s)
- Chathura D. Suraweera
- Genome Sciences and Cancer Division, The John Curtin School of Medical Research, Australian National University, Canberra 2601, Australia;
| | - Benjamin Espinoza
- Department of Biochemistry and Chemistry, La Trobe University, Melbourne, VIC 3086, Australia;
| | - Mark G. Hinds
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Marc Kvansakul
- Genome Sciences and Cancer Division, The John Curtin School of Medical Research, Australian National University, Canberra 2601, Australia;
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5
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Monzón S, Varona S, Negredo A, Vidal-Freire S, Patiño-Galindo JA, Ferressini-Gerpe N, Zaballos A, Orviz E, Ayerdi O, Muñoz-Gómez A, Delgado-Iribarren A, Estrada V, García C, Molero F, Sánchez-Mora P, Torres M, Vázquez A, Galán JC, Torres I, Causse Del Río M, Merino-Diaz L, López M, Galar A, Cardeñoso L, Gutiérrez A, Loras C, Escribano I, Alvarez-Argüelles ME, Del Río L, Simón M, Meléndez MA, Camacho J, Herrero L, Jiménez P, Navarro-Rico ML, Jado I, Giannetti E, Kuhn JH, Sanchez-Lockhart M, Di Paola N, Kugelman JR, Guerra S, García-Sastre A, Cuesta I, Sánchez-Seco MP, Palacios G. Monkeypox virus genomic accordion strategies. Nat Commun 2024; 15:3059. [PMID: 38637500 PMCID: PMC11026394 DOI: 10.1038/s41467-024-46949-7] [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: 09/06/2023] [Accepted: 03/14/2024] [Indexed: 04/20/2024] Open
Abstract
The 2023 monkeypox (mpox) epidemic was caused by a subclade IIb descendant of a monkeypox virus (MPXV) lineage traced back to Nigeria in 1971. Person-to-person transmission appears higher than for clade I or subclade IIa MPXV, possibly caused by genomic changes in subclade IIb MPXV. Key genomic changes could occur in the genome's low-complexity regions (LCRs), which are challenging to sequence and are often dismissed as uninformative. Here, using a combination of highly sensitive techniques, we determine a high-quality MPXV genome sequence of a representative of the current epidemic with LCRs resolved at unprecedented accuracy. This reveals significant variation in short tandem repeats within LCRs. We demonstrate that LCR entropy in the MPXV genome is significantly higher than that of single-nucleotide polymorphisms (SNPs) and that LCRs are not randomly distributed. In silico analyses indicate that expression, translation, stability, or function of MPXV orthologous poxvirus genes (OPGs), including OPG153, OPG204, and OPG208, could be affected in a manner consistent with the established "genomic accordion" evolutionary strategies of orthopoxviruses. We posit that genomic studies focusing on phenotypic MPXV differences should consider LCR variability.
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Affiliation(s)
- Sara Monzón
- Unidad de Bioinformática, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Sarai Varona
- Unidad de Bioinformática, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Escuela Internacional de Doctorado de la UNED (EIDUNED), Universidad Nacional de Educación a Distancia (UNED), 2832, Madrid, Spain
| | - Anabel Negredo
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Santiago Vidal-Freire
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | | | - Angel Zaballos
- Unidad de Genómica, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Eva Orviz
- Centro Sanitario Sandoval, Hospital Clínico San Carlos, 28040, Madrid, Spain
| | - Oskar Ayerdi
- Centro Sanitario Sandoval, Hospital Clínico San Carlos, 28040, Madrid, Spain
| | - Ana Muñoz-Gómez
- Centro Sanitario Sandoval, Hospital Clínico San Carlos, 28040, Madrid, Spain
| | | | - Vicente Estrada
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro Sanitario Sandoval, Hospital Clínico San Carlos, 28040, Madrid, Spain
| | - Cristina García
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Francisca Molero
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Patricia Sánchez-Mora
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Montserrat Torres
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Ana Vázquez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Juan-Carlos Galán
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain
| | - Ignacio Torres
- Servicio de Microbiología, Hospital Clínico Universitario, Instituto de Investigación INCLIVA, 46010, Valencia, Spain
| | - Manuel Causse Del Río
- Unidad de Microbiología, Hospital Universitario Reina Sofía, Instituto Maimónides de Investigación Biomédica de Córdoba, 14004, Córdoba, Spain
| | - Laura Merino-Diaz
- Unidad Clínico de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del Rocío, 41013, Sevilla, Spain
| | - Marcos López
- Servicio de Microbiología y Parasitología, Hospital Universitario Puerta de Hierro Majadahonda, 28222, Madrid, Spain
| | - Alicia Galar
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, 28007, Madrid, Spain
| | - Laura Cardeñoso
- Servicio de Microbiología, Instituto de Investigación Sanitaria, Hospital Universitario de la Princesa, 28006, Madrid, Spain
| | - Almudena Gutiérrez
- Servicio de Microbiología y Parasitología Clínica, Hospital Universitario La Paz, 28046, Madrid, Spain
| | - Cristina Loras
- Servicio de Microbiología, Hospital General y Universitario, 13005, Ciudad Real, Spain
| | - Isabel Escribano
- Servicio de Microbiología, Hospital General Universitario Dr. Balmis, 03010, Alicante, Spain
| | | | | | - María Simón
- Servicio de Microbiología, Hospital Central de la Defensa "Gómez Ulla", 28947, Madrid, Spain
| | - María Angeles Meléndez
- Servicio de Microbiología y Parasitología, Hospital Universitario 12 de Octubre, 28041, Madrid, Spain
| | - Juan Camacho
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Laura Herrero
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Pilar Jiménez
- Unidad de Genómica, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - María Luisa Navarro-Rico
- Unidad de Genómica, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Isabel Jado
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Elaina Giannetti
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, 21702, USA
| | - Mariano Sanchez-Lockhart
- United States Army Research Institute for Infectious Disease, Fort Detrick, Frederick, MD, 21702, USA
| | - Nicholas Di Paola
- United States Army Research Institute for Infectious Disease, Fort Detrick, Frederick, MD, 21702, USA
| | - Jeffrey R Kugelman
- United States Army Research Institute for Infectious Disease, Fort Detrick, Frederick, MD, 21702, USA
| | - Susana Guerra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Departmento de Medicina Preventiva, Salud Publica y Microbiología, Universidad Autónoma de Madrid, 28029, Madrid, Spain
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Isabel Cuesta
- Unidad de Bioinformática, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Maripaz P Sánchez-Seco
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Gustavo Palacios
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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6
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Alakunle E, Kolawole D, Diaz-Cánova D, Alele F, Adegboye O, Moens U, Okeke MI. A comprehensive review of monkeypox virus and mpox characteristics. Front Cell Infect Microbiol 2024; 14:1360586. [PMID: 38510963 PMCID: PMC10952103 DOI: 10.3389/fcimb.2024.1360586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
Monkeypox virus (MPXV) is the etiological agent of monkeypox (mpox), a zoonotic disease. MPXV is endemic in the forested regions of West and Central Africa, but the virus has recently spread globally, causing outbreaks in multiple non-endemic countries. In this paper, we review the characteristics of the virus, including its ecology, genomics, infection biology, and evolution. We estimate by phylogenomic molecular clock that the B.1 lineage responsible for the 2022 mpox outbreaks has been in circulation since 2016. We interrogate the host-virus interactions that modulate the virus infection biology, signal transduction, pathogenesis, and host immune responses. We highlight the changing pathophysiology and epidemiology of MPXV and summarize recent advances in the prevention and treatment of mpox. In addition, this review identifies knowledge gaps with respect to the virus and the disease, suggests future research directions to address the knowledge gaps, and proposes a One Health approach as an effective strategy to prevent current and future epidemics of mpox.
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Affiliation(s)
- Emmanuel Alakunle
- Department of Natural and Environmental Sciences, American University of Nigeria, Yola, Nigeria
| | - Daniel Kolawole
- Department of Natural and Environmental Sciences, American University of Nigeria, Yola, Nigeria
| | - Diana Diaz-Cánova
- Department of Medical Biology, UIT – The Arctic University of Norway, Tromsø, Norway
| | - Faith Alele
- School of Health, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Oyelola Adegboye
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Ugo Moens
- Department of Medical Biology, UIT – The Arctic University of Norway, Tromsø, Norway
| | - Malachy Ifeanyi Okeke
- Department of Natural and Environmental Sciences, American University of Nigeria, Yola, Nigeria
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7
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Desingu PA, Rubeni TP, Nagarajan K, Sundaresan NR. Molecular evolution of 2022 multi-country outbreak-causing monkeypox virus Clade IIb. iScience 2024; 27:108601. [PMID: 38188513 PMCID: PMC10770499 DOI: 10.1016/j.isci.2023.108601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 09/16/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
The monkeypox virus (Mpoxv) Clade IIb viruses that caused an outbreak in 2017-18 in Nigeria and its genetically related viruses have been detected in many countries and caused multi-country outbreak in 2022. Since the pandemic-causing Mpoxv Clade IIb viruses are closely related to Clade IIa viruses which mostly cause endemic, the Clade IIb Mpoxv might have certain specific genetic variations that are still largely unknown. Here, we have systematically analyzed genetic alterations in different clades of Mpox viruses. The results suggest that the Mpoxv Clade IIb have genetic variations in terms of genomic gaps, frameshift mutations, in-frame nonsense mutations, amino acid tandem repeats, and APOBEC3 mutations. Further, we observed specific genetic variations in the multiple genes specific for Clade I and Clade IIb, and exclusive genetic variations for Clade IIa and Clade IIb. Collectively, findings shed light on the evolution and genetic variations in the outbreak of 2022 causing Mpoxv Clade IIb.
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Affiliation(s)
- Perumal Arumugam Desingu
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | | | - K. Nagarajan
- Department of Veterinary Pathology, Madras Veterinary College, Vepery, Chennai 600007, Tamil Nadu
- Veterinary and Animal Sciences University (TANUVAS)
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8
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Shah BM, Modi P. Breaking Barriers: Current Advances and Future Directions in Mpox Therapy. Curr Drug Targets 2024; 25:62-76. [PMID: 38151842 DOI: 10.2174/0113894501281263231218070841] [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: 09/08/2023] [Revised: 11/21/2023] [Accepted: 11/28/2023] [Indexed: 12/29/2023]
Abstract
BACKGROUND Mpox, a newly discovered zoonotic infection, can be transmitted from animal to human and between humans. Serological and genomic studies are used to identify the virus. OBJECTIVE Currently, there are no proven effective treatments for Mpox. Also, the safety and efficacy of intravenous vaccinia immune globulin, oral Tecovirimat (an inhibitor of intracellular viral release), and oral Brincidofovir (a DNA polymerase inhibitor) against the Mpox virus are uncertain, highlighting the need for more effective and safe treatments. As a result, drug repurposing has emerged as a promising strategy to identify previously licensed drugs that can be repurposed to treat Mpox. RESULTS Various approaches have been employed to identify previously approved drugs that can target specific Mpox virus proteins, including thymidylate kinase, D9 decapping enzyme, E8 protein, Topoisomerase1, p37, envelope proteins (D13, A26, and H3), F13 protein, virus's main cysteine proteases, and DNA polymerase. CONCLUSION In this summary, we provide an overview of potential drugs that could be used to treat Mpox and discuss the underlying biological processes of their actions.
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Affiliation(s)
- Bhumi M Shah
- Department of Pharmaceutical Chemistry, L.J. Institute of Pharmacy, L.J. University, Ahmedabad, Gujarat 382210, India
| | - Palmi Modi
- Department of Pharmaceutical Chemistry, L.J. Institute of Pharmacy, L.J. University, Ahmedabad, Gujarat 382210, India
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9
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Schuele L, Boter M, Nieuwenhuijse DF, Götz H, Fanoy E, de Vries H, Vieyra B, Bavalia R, Hoornenborg E, Molenkamp R, Jonges M, van den Ouden A, Simões M, van den Lubben M, Koopmans M, Welkers MRA, Oude Munnink BB. Circulation, viral diversity and genomic rearrangement in mpox virus in the Netherlands during the 2022 outbreak and beyond. J Med Virol 2024; 96:e29397. [PMID: 38235923 DOI: 10.1002/jmv.29397] [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: 08/31/2023] [Revised: 11/23/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
Abstract
Mpox is an emerging zoonotic disease which has now spread to over 113 countries as of August 2023, with over 89,500 confirmed human cases. The Netherlands had one of the highest incidence rates in Europe during the peak of the outbreak. In this study, we generated 158 near-complete mpox virus (MPXV) genomes (12.4% of nationwide cases) that were collected throughout the Netherlands from the start of the outbreak in May 2022 to August 2023 to track viral evolution and investigate outbreak dynamics. We detected 14 different viral lineages, suggesting multiple introductions followed by rapid initial spread within the country. The estimated evolutionary rate was relatively high compared to previously described in orthopoxvirus literature, with an estimated 11.58 mutations per year. Genomic rearrangement events occurred at a rate of 0.63% and featured a large deletion event. In addition, based on phylogenetics, we identified multiple potential transmission clusters which could be supported by direct source- and contact tracing data. This led to the identification of at least two main transmission locations at the beginning of the outbreak. We conclude that whole genome sequencing of MPXV is essential to enhance our understanding of outbreak dynamics and evolution of a relatively understudied and emerging zoonotic pathogen.
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Affiliation(s)
- Leonard Schuele
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Marjan Boter
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - David F Nieuwenhuijse
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Hannelore Götz
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
- Department of Public Health, (Infectious Disease Control and Center Sexual Health) Public Health Service Rotterdam-Rijnmond, Rotterdam, Netherlands
| | - Ewout Fanoy
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, Netherlands
| | - Henry de Vries
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, Netherlands
- Department of Dermatology, Amsterdam UMC, Location University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunology, Infectious Diseases, Amsterdam, Netherlands
| | - Bruno Vieyra
- Department of Public Health, (Infectious Disease Control and Center Sexual Health) Public Health Service Rotterdam-Rijnmond, Rotterdam, Netherlands
| | - Roisin Bavalia
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, Netherlands
| | - Elske Hoornenborg
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunology, Infectious Diseases, Amsterdam, Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Marcel Jonges
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC location AMC, University of Amsterdam, Amsterdam, Netherlands
| | | | - Margarida Simões
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
- European Program for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control, (ECDC), Stockholm, Sweden
| | - Mariken van den Lubben
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, Netherlands
| | - Marion Koopmans
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Matthijs R A Welkers
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, Netherlands
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
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10
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Brusati A, Agostinetto G, Bruno A, Casiraghi M, Pescini D, Sandionigi A, Balech B. Exploration and Retrieval of Virus-Related Molecular Data Using ExTaxsI: The Monkeypox Use Case. Methods Mol Biol 2024; 2732:145-154. [PMID: 38060123 DOI: 10.1007/978-1-0716-3515-5_10] [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: 12/08/2023]
Abstract
Retrieval and visualization of biological data are essential for understanding complex systems. With the increasing volume of data generated from high-throughput sequencing technologies, effective and optimized data visualization tools have become indispensable. This is particularly relevant in the COVID-19 postpandemic period, where understanding the diversity and interactions of microbial communities (i.e., viral and bacterial) constitutes an important asset to develop and plan suitable interventions.In this chapter, we show the usage and the potentials of ExTaxsI (Exploring Taxonomy Information) tool to retrieve viral biodiversity data stored in National Center for Biotechnology Information (NCBI) databases and create the related visualization. In addition, by integrating different functions and modules, the tool generates relevant types of visualization plots to facilitate the exploration of microbial biodiversity communities useful to deep dive into ecological and taxonomic relationships among different species and identify potential significant targets.Using the Monkeypox virus as a case study, this work points out significant perspectives on biological data visualization, which can be used to gain insights into the ecology, evolution, and pathogenesis of viruses. Accordingly, we show the potentiality of ExTaxsI to organize and describe the available/downloaded data in an easy, simple, and interpretable way allowing the user to interact dynamically with the visualization plots through specific filters, zoom, and explore functions.
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Affiliation(s)
- Alberto Brusati
- University of Pavia, Department of Brain and Behavioral Sciences, Pavia, Italy
| | - Giulia Agostinetto
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Milan, Italy.
| | - Antonia Bruno
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Milan, Italy
| | - Maurizio Casiraghi
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Milan, Italy
| | - Dario Pescini
- University of Milano-Bicocca, Department of Statistics and Quantitative Methods, Milan, Italy
| | - Anna Sandionigi
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Milan, Italy
- Quantia Consulting srl, Department of Data Science and Education, Remote Company, Milan, Italy
| | - Bachir Balech
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (CNR), Bari, Italy
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11
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Gómez-Sánchez I, Castelán-Sánchez HG, Martínez-Castilla LP, Hurtado-Ramírez JM, López-Leal G. Genetic insights into the microevolutionary dynamics and early introductions of human monkeypox virus in Mexico. Arch Virol 2023; 169:2. [PMID: 38070010 DOI: 10.1007/s00705-023-05936-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/31/2023] [Indexed: 12/18/2023]
Abstract
The recent global outbreak of mpox, caused by monkeypox virus (MPV) emerged in Europe in 2022 and rapidly spread to over 40 countries. The Americas are currently facing the highest impact, reporting over 50,000 cases by early 2023. In this study, we analyzed 880 MPV isolates worldwide to gain insights into the evolutionary patterns and initial introduction events of the virus in Mexico. We found that MPV entered Mexico on multiple occasions, from the United Kingdom, Portugal, and Canada, and subsequently spread locally in different regions of Mexico. Additionally, we show that MPV has an open pangenome, highlighting the role of gene turnover in shaping its genomic diversity, rather than single-nucleotide polymorphisms (SNPs), which do not contribute significantly to genome diversity. Although the genome contains multiple SNPs in coding regions, these remain under purifying selection, suggesting their evolutionary conservation. One notable exception is amino acid position 63 of the protein encoded by the Cop-A4L gene, which is intricately related to viral maturity, which we found to be under strong positive selection. Ancestral state reconstruction indicated that the ancestral state at position 63 corresponds to the amino acid valine, which is present only in isolates of clade I. However, the isolates from the current outbreak contained threonine at position 63. Our findings contribute new information about the evolution of monkeypox virus.
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Affiliation(s)
- Israel Gómez-Sánchez
- Laboratorio de Biología Computacional y Virómica Integrativa, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Hugo G Castelán-Sánchez
- Grupo de Genómica y Dinámica Evolutiva de Microorganismos EmergentesPrograma de Investigadoras e Investigadores por México, Consejo Nacional de Ciencia y Tecnología, Mexico City, Mexico.
| | - León P Martínez-Castilla
- Grupo de Genómica y Dinámica Evolutiva de Microorganismos EmergentesPrograma de Investigadoras e Investigadores por México, Consejo Nacional de Ciencia y Tecnología, Mexico City, Mexico
| | | | - Gamaliel López-Leal
- Laboratorio de Biología Computacional y Virómica Integrativa, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico.
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12
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Desingu PA, Rubeni TP, Nagarajan K, Sundaresan NR. Sign of APOBEC editing, purifying selection, frameshift, and in-frame nonsense mutations in the microevolution of lumpy skin disease virus. Front Microbiol 2023; 14:1214414. [PMID: 38033577 PMCID: PMC10682384 DOI: 10.3389/fmicb.2023.1214414] [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: 04/29/2023] [Accepted: 10/25/2023] [Indexed: 12/02/2023] Open
Abstract
The lumpy skin disease virus (LSDV), which mostly affects ruminants and causes huge-economic loss, was endemic in Africa, caused outbreaks in the Middle East, and was recently detected in Russia, Serbia, Greece, Bulgaria, Kazakhstan, China, Taiwan, Vietnam, Thailand, and India. However, the role of evolutionary drivers such as codon selection, negative/purifying selection, APOBEC editing, and genetic variations such as frameshift and in-frame nonsense mutations in the LSDVs, which cause outbreaks in cattle in various countries, are still largely unknown. In the present study, a frameshift mutation in LSDV035, LSDV019, LSDV134, and LSDV144 genes and in-frame non-sense mutations in LSDV026, LSDV086, LSDV087, LSDV114, LSDV130, LSDV131, LSDV145, LSDV154, LSDV155, LSDV057, and LSDV081 genes were revealed among different clusters. Based on the available complete genome sequences, the prototype wild-type cluster-1.2.1 virus has been found in other than Africa only in India, the wild-type cluster-1.2.2 virus found in Africa were spread outside Africa, and the recombinant viruses spreading only in Asia and Russia. Although LSD viruses circulating in different countries form a specific cluster, the viruses detected in each specific country are distinguished by frameshift and in-frame nonsense mutations. Furthermore, the present study has brought to light that the selection pressure for codons usage bias is mostly exerted by purifying selection, and this process is possibly caused by APOBEC editing. Overall, the present study sheds light on microevolutions in LSDV, expected to help in future studies towards disturbed ORFs, epidemiological diagnostics, attenuation/vaccine reverts, and predicting the evolutionary direction of LSDVs.
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Affiliation(s)
| | - T. P. Rubeni
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - K. Nagarajan
- Department of Veterinary Pathology, Madras Veterinary College, Chennai, India
- Veterinary and Animal Sciences University (TANUVAS), Chennai, India
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13
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Rigou S, Schmitt A, Alempic JM, Lartigue A, Vendloczki P, Abergel C, Claverie JM, Legendre M. Pithoviruses Are Invaded by Repeats That Contribute to Their Evolution and Divergence from Cedratviruses. Mol Biol Evol 2023; 40:msad244. [PMID: 37950899 PMCID: PMC10664404 DOI: 10.1093/molbev/msad244] [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: 02/25/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 11/13/2023] Open
Abstract
Pithoviridae are amoeba-infecting giant viruses possessing the largest viral particles known so far. Since the discovery of Pithovirus sibericum, recovered from a 30,000-yr-old permafrost sample, other pithoviruses, and related cedratviruses, were isolated from various terrestrial and aquatic samples. Here, we report the isolation and genome sequencing of 2 Pithoviridae from soil samples, in addition to 3 other recent isolates. Using the 12 available genome sequences, we conducted a thorough comparative genomic study of the Pithoviridae family to decipher the organization and evolution of their genomes. Our study reveals a nonuniform genome organization in 2 main regions: 1 concentrating core genes and another gene duplications. We also found that Pithoviridae genomes are more conservative than other families of giant viruses, with a low and stable proportion (5% to 7%) of genes originating from horizontal transfers. Genome size variation within the family is mainly due to variations in gene duplication rates (from 14% to 28%) and massive invasion by inverted repeats. While these repeated elements are absent from cedratviruses, repeat-rich regions cover as much as a quarter of the pithoviruses genomes. These regions, identified using a dedicated pipeline, are hotspots of mutations, gene capture events, and genomic rearrangements that contribute to their evolution.
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Affiliation(s)
- Sofia Rigou
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Alain Schmitt
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Jean-Marie Alempic
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Audrey Lartigue
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Peter Vendloczki
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Chantal Abergel
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Jean-Michel Claverie
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Matthieu Legendre
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
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14
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Colson P, Bader W, Fantini J, Dudouet P, Levasseur A, Pontarotti P, Devaux C, Raoult D. From viral democratic genomes to viral wild bunch of quasispecies. J Med Virol 2023; 95:e29209. [PMID: 37937701 DOI: 10.1002/jmv.29209] [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: 08/07/2023] [Revised: 10/05/2023] [Accepted: 10/19/2023] [Indexed: 11/09/2023]
Abstract
The tremendous majority of RNA genomes from pathogenic viruses analyzed and deposited in databases are consensus or "democratic" genomes. They represent the genomes most frequently found in the clinical samples of patients but do not account for the huge genetic diversity of coexisting genomes, which is better described as quasispecies. A viral quasispecies is defined as the dynamic distribution of nonidentical but closely related mutants, variants, recombinant, or reassortant viral genomes. Viral quasispecies have collective behavior and dynamics and are the subject of internal interactions that comprise interference, complementation, or cooperation. In the setting of SARS-CoV-2 infection, intrahost SARS-CoV-2 genetic diversity was recently notably reported for immunocompromised, chronically infected patients, for patients treated with monoclonal antibodies targeting the viral spike protein, and for different body compartments of a single patient. A question that deserves attention is whether such diversity is generated postinfection from a clonal genome in response to selection pressure or is already present at the time of infection as a quasispecies. In the present review, we summarize the data supporting that hosts are infected by a "wild bunch" of viruses rather than by multiple virions sharing the same genome. Each virion in the "wild bunch" may have different virulence and tissue tropisms. As the number of viruses replicated during host infections is huge, a viral quasispecies at any time of infection is wide and is also influenced by host-specific selection pressure after infection, which accounts for the difficulty in deciphering and predicting the appearance of more fit variants and the evolution of epidemics of novel RNA viruses.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Wahiba Bader
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Jacques Fantini
- INSERM UMR_S 1072, Aix-Marseille Université, Marseille, France
| | - Pierre Dudouet
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Pierre Pontarotti
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS)-SNC5039, Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS)-SNC5039, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
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15
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Souza ARV, Brinkmann A, Esparza J, Nitsche A, Damaso CR. Gene duplication, gene loss, and recombination events with variola virus shaped the complex evolutionary path of historical American horsepox-based smallpox vaccines. mBio 2023; 14:e0188723. [PMID: 37729584 PMCID: PMC10653919 DOI: 10.1128/mbio.01887-23] [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: 07/18/2023] [Accepted: 07/28/2023] [Indexed: 09/22/2023] Open
Abstract
IMPORTANCE Modern smallpox vaccines, such as those used against mpox, are made from vaccinia viruses, but it is still unknown whether cowpox, horsepox, or vaccinia viruses were used in the early 20th century or earlier. The mystery began to be solved when the genomes of six historical smallpox vaccines used in the United States from 1850 to 1902 were determined. Our work analyzed in detail the genomes of these six historical vaccines, revealing a complex genomic structure. Historical vaccines are highly similar to horsepox in the core of their genomes, but some are closer to the structure of vaccinia virus at the ends of the genome. One of the vaccines is a recombinant virus with parts of variola virus recombined into its genome. Our data add valuable information for understanding the evolutionary path of current smallpox vaccines and the genetic makeup of the potentially extinct group of horsepox viruses.
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Affiliation(s)
- Aline R. V. Souza
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Annika Brinkmann
- Centre for Biological Threats and Special Pathogens 1 – Highly Pathogenic Viruses & German Consultant Laboratory for Poxviruses & WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - José Esparza
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens 1 – Highly Pathogenic Viruses & German Consultant Laboratory for Poxviruses & WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Clarissa R. Damaso
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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16
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Tseng KK, Koehler H, Becker DJ, Gibb R, Carlson CJ, Fernandez MDP, Seifert SN. Viral genomic features predict orthopoxvirus reservoir hosts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.564211. [PMID: 37961540 PMCID: PMC10634857 DOI: 10.1101/2023.10.26.564211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Orthopoxviruses (OPVs), including the causative agents of smallpox and mpox have led to devastating outbreaks in human populations worldwide. However, the discontinuation of smallpox vaccination, which also provides cross-protection against related OPVs, has diminished global immunity to OPVs more broadly. We apply machine learning models incorporating both host ecological and viral genomic features to predict likely reservoirs of OPVs. We demonstrate that incorporating viral genomic features in addition to host ecological traits enhanced the accuracy of potential OPV host predictions, highlighting the importance of host-virus molecular interactions in predicting potential host species. We identify hotspots for geographic regions rich with potential OPV hosts in parts of southeast Asia, equatorial Africa, and the Amazon, revealing high overlap between regions predicted to have a high number of potential OPV host species and those with the lowest smallpox vaccination coverage, indicating a heightened risk for the emergence or establishment of zoonotic OPVs. Our findings can be used to target wildlife surveillance, particularly related to concerns about mpox establishment beyond its historical range.
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Affiliation(s)
- Katie K. Tseng
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, USA
| | - Heather Koehler
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Daniel J. Becker
- Department of Biology, School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Rory Gibb
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK
- People & Nature Lab, UCL East, University College London, Stratford, London, UK
| | - Colin J. Carlson
- Center for Global Health Science and Security, Georgetown University, Washington, DC, USA
| | | | - Stephanie N. Seifert
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, USA
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17
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Akaishi T. Recently Added Frameshift Mutation in Human Monkeypox Virus (hMPXV) OPG191 Gene. TOHOKU J EXP MED 2023; 261:103-107. [PMID: 37438121 DOI: 10.1620/tjem.2023.j057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Human monkeypox virus (hMPXV) has caused sporadic outbreaks intermittently across countries in recent years, with the largest outbreak in 2022. However, the underlying mechanisms remain unclear. This study searched for recently developed structural variants of the viral genome. A total of 22 hMPXV whole genome sequences were randomly selected from the National Center for Biotechnology Information GenBank sequence database for initial screening. As a result, a recent frameshift mutation based on a 2-base insertion in a coding region was identified at the 3' terminal of the OPG191 gene, which encodes MPXVgp168 (B7R) protein. With this insertion, the protein was prematurely truncated, and the last 11 amino acids were missing, with 3 alternative amino acids added. Among the hMPXV genome sequences registered in the GenBank database as of January 2023, 61 sequences lacked the 2-base insertion and 3,362 sequences were inserted. All 61 sequences without mutations were collected before 2020, whereas 3,358 (99.9%) of the 3,362 sequences with the insertion were collected during or after 2022. These findings imply that a 2-base insertion has recently emerged and has been fixed among the virus population that prevailed in 2022. In summary, a recently emerged frameshift mutation with a 2-base insertion was identified in hMPXV OPG191 gene. Although the structural and functional consequences of this mutation on virulence and infectivity are unknown, research on the possible associations between this mutation and recent hMPXV outbreaks is warranted.
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Affiliation(s)
- Tetsuya Akaishi
- Department of Education and Support for Regional Medicine, Tohoku University
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18
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Freyn AW, Atyeo C, Earl PL, Americo JL, Chuang GY, Natarajan H, Frey TR, Gall JG, Moliva JI, Hunegnaw R, Asthagiri Arunkumar G, Ogega CO, Nasir A, Santos G, Levin RH, Meni A, Jorquera PA, Bennett H, Johnson JA, Durney MA, Stewart-Jones G, Hooper JW, Colpitts TM, Alter G, Sullivan NJ, Carfi A, Moss B. An mpox virus mRNA-lipid nanoparticle vaccine confers protection against lethal orthopoxviral challenge. Sci Transl Med 2023; 15:eadg3540. [PMID: 37792954 DOI: 10.1126/scitranslmed.adg3540] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 08/18/2023] [Indexed: 10/06/2023]
Abstract
Mpox virus (MPXV) caused a global outbreak in 2022. Although smallpox vaccines were rapidly deployed to curb spread and disease among those at highest risk, breakthrough disease was noted after complete immunization. Given the threat of additional zoonotic events and the virus's evolving ability to drive human-to-human transmission, there is an urgent need for an MPXV-specific vaccine that confers protection against evolving MPXV strains and related orthopoxviruses. Here, we demonstrate that an mRNA-lipid nanoparticle vaccine encoding a set of four highly conserved MPXV surface proteins involved in virus attachment, entry, and transmission can induce MPXV-specific immunity and heterologous protection against a lethal vaccinia virus (VACV) challenge. Compared with modified vaccinia virus Ankara (MVA), which forms the basis for the current MPXV vaccine, immunization with an mRNA-based MPXV vaccine generated superior neutralizing activity against MPXV and VACV and more efficiently inhibited spread between cells. We also observed greater Fc effector TH1-biased humoral immunity to the four MPXV antigens encoded by the vaccine, as well as to the four VACV homologs. Single MPXV antigen-encoding mRNA vaccines provided partial protection against VACV challenge, whereas multivalent vaccines combining mRNAs encoding two, three, or four MPXV antigens protected against disease-related weight loss and death equal or superior to MVA vaccination. These data demonstrate that an mRNA-based MPXV vaccine confers robust protection against VACV.
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Affiliation(s)
| | | | - Patricia L Earl
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, 20892 MD, USA
| | - Jeffrey L Americo
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, 20892 MD, USA
| | | | | | | | - Jason G Gall
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, 20892 MD, USA
| | - Juan I Moliva
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, 20892 MD, USA
| | - Ruth Hunegnaw
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, 20892 MD, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Jay W Hooper
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, 21702 MD, USA
| | | | | | - Nancy J Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, 20892 MD, USA
| | | | - Bernard Moss
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, 20892 MD, USA
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19
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Molteni C, Forni D, Cagliani R, Bravo IG, Sironi M. Evolution and diversity of nucleotide and dinucleotide composition in poxviruses. J Gen Virol 2023; 104. [PMID: 37792576 DOI: 10.1099/jgv.0.001897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023] Open
Abstract
Poxviruses (family Poxviridae) have long dsDNA genomes and infect a wide range of hosts, including insects, birds, reptiles and mammals. These viruses have substantial incidence, prevalence and disease burden in humans and in other animals. Nucleotide and dinucleotide composition, mostly CpG and TpA, have been largely studied in viral genomes because of their evolutionary and functional implications. We analysed here the nucleotide and dinucleotide composition, as well as codon usage bias, of a set of representative poxvirus genomes, with a very diverse host spectrum. After correcting for overall nucleotide composition, entomopoxviruses displayed low overall GC content, no enrichment in TpA and large variation in CpG enrichment, while chordopoxviruses showed large variation in nucleotide composition, no obvious depletion in CpG and a weak trend for TpA depletion in GC-rich genomes. Overall, intergenome variation in dinucleotide composition in poxviruses is largely accounted for by variation in overall genomic GC levels. Nonetheless, using vaccinia virus as a model, we found that genes expressed at the earliest times in infection are more CpG-depleted than genes expressed at later stages. This observation has parallels in betahepesviruses (also large dsDNA viruses) and suggests an antiviral role for the innate immune system (e.g. via the zinc-finger antiviral protein ZAP) in the early phases of poxvirus infection. We also analysed codon usage bias in poxviruses and we observed that it is mostly determined by genomic GC content, and that stratification after host taxonomy does not contribute to explaining codon usage bias diversity. By analysis of within-species diversity, we show that genomic GC content is the result of mutational biases. Poxvirus genomes that encode a DNA ligase are significantly AT-richer than those that do not, suggesting that DNA repair systems shape mutation biases. Our data shed light on the evolution of poxviruses and inform strategies for their genetic manipulation for therapeutic purposes.
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Affiliation(s)
- Cristian Molteni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Ignacio G Bravo
- Laboratoire MIVEGEC (Univ Montpellier CNRS, IRD), Centre National de la Recherche Scientifique, Montpellier, France
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
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20
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Colson P, Delerce J, Fantini J, Pontarotti P, La Scola B, Raoult D. The return of the "Mistigri" (virus adaptative gain by gene loss) through the SARS-CoV-2 XBB.1.5 chimera that predominated in 2023. J Med Virol 2023; 95:e29146. [PMID: 37800455 DOI: 10.1002/jmv.29146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/03/2023] [Accepted: 09/19/2023] [Indexed: 10/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 XBB.1.5 is the first recombinant lineage to predominate at the country and global scales. Very interestingly, like the Marseille-4B subvariant (or B.1.160) and the pandemic variant B.1.1.7 (or Alpha) previously, it has its ORF8 gene inactivated by a stop codon. We aimed here to study the distribution of stop codons in ORF8 of XBB.1.5 and non-XBB.1.5 genomes. We identified that a stop codon was present at 89 (74%) ORF8 codons in ≥1 of 15 222 404 genomes available in GISAID. The mean proportion of genomes with a stop codon per codon was 0.11% (range, 0%-7.8%). In addition, a stop codon was detected at 15 (12%) codons in at least 1000 genomes. These 15 codons are notably located on seven stem-loop hairpin regions and in the signal peptide region for the case of the XBB.1.5 lineage (codon 8). Thus, it is very likely that stop codons in ORF8 gene contributed on at least three occasions and independently during the pandemic to the evolutionary success of a lineage that became transiently predominant. Such association of gene loss with evolutionary success, which suits the recently described Mistigri rule, is an important biological phenomenon very unknown in virology while largely described in cellular organisms.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | | | - Jacques Fantini
- INSERM UMR_S 1072, Aix-Marseille Université, Marseille, France
| | - Pierre Pontarotti
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- Department of Biological Sciences, Centre National de la Recherche Scientifique (CNRS)-SNC5039, Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
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21
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Andrei G, Snoeck R. Differences in pathogenicity among the mpox virus clades: impact on drug discovery and vaccine development. Trends Pharmacol Sci 2023; 44:719-739. [PMID: 37673695 DOI: 10.1016/j.tips.2023.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/11/2023] [Accepted: 08/11/2023] [Indexed: 09/08/2023]
Abstract
Since May 2022, mpox virus (MPXV) has attracted considerable attention due to a multi-country outbreak. Marked differences in epidemiology, transmission, and pathology between the 2022 global mpox outbreak (clade IIb) and classical mpox disease, endemic in Africa (clades I and IIa) have been highlighted. MPXV genome analysis has identified the genomic changes characterizing clade IIb and the drivers of MPXV rapid evolution. Although mpox cases have largely declined, MPXV cryptic transmission and microevolution continues, which may lead to an MPXV of unpredictable pathogenicity. Vaccines and antivirals developed against variola virus, the agent that caused the extinguished plague smallpox, have been used to contain the 2022 mpox outbreak. In this review article, recent findings on MPXV origin and evolution and relevant models able to recapitulate differences in MPXV pathogenicity, which are important for drug and vaccine development, are discussed.
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Affiliation(s)
- Graciela Andrei
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
| | - Robert Snoeck
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
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22
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Garcia-Junior MA, Andrade BS, Guevara-Vega M, de Melo IS, Cunha TM, Jardim ACG, Sabino-Silva R. Oral Infection, Oral Pathology and Salivary Diagnostics of Mpox Disease: Relevance in Dentistry and OMICs Perspectives. Int J Mol Sci 2023; 24:14362. [PMID: 37762664 PMCID: PMC10531708 DOI: 10.3390/ijms241814362] [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: 07/25/2023] [Revised: 08/31/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
In this narrative review, we aim to point out the close relationship between mpox virus (MPXV) infection and the role of saliva as a diagnostic tool for mpox, considering the current molecular approach and in the perspective of OMICs application. The MPXV uses the host cell's rough endoplasmic reticulum, ribosomes, and cytoplasmic proteins to replicate its genome and synthesize virions for cellular exit. The presence of oral mucosa lesions associated with mpox infection is one of the first signs of infection; however, current diagnostic tools find it difficult to detect the virus before the rashes begin. MPXV transmission occurs through direct contact with an infected lesion and infected body fluids, including saliva, presenting a potential use of this fluid for diagnostic purposes. Currently available diagnostic tests for MPXV detection are performed either by real-time quantitative PCR (RT-qPCR) or ELISA, which presents several limitations since they are invasive tests. Despite current clinical trials with restricted sample size, MPXV DNA was detected in saliva with a sensitivity of 85%-100%. In this context, the application of transcriptomics, metabolomics, lipidomics, or proteomics analyses coupled with saliva can identify novel disease biomarkers. Thus, it is important to note that the identification and quantification of salivary DNA, RNA, lipid, protein, and metabolite can provide novel non-invasive biomarkers through the use of OMICs platforms aiding in the early detection and diagnosis of MPXV infection. Untargeted mass spectrometry (MS)-based proteomics reveals that some proteins also expressed in saliva were detected with greater expression differences in blood plasma when comparing mpox patients and healthy subjects, suggesting a promising alternative to be applied in screening or diagnostic platforms for mpox salivary diagnostics coupled to OMICs.
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Affiliation(s)
- Marcelo Augusto Garcia-Junior
- Innovation Center in Salivary Diagnostics and Nanobiotechnology, Laboratory of Nanobiotechnology – “Luiz Ricardo Goulart”, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlândia 38496-017, Brazil (M.G.-V.)
| | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, Department of Biological Sciences, State University of Southwest of Bahia (UESB), Jequié 45083-900, Brazil
| | - Marco Guevara-Vega
- Innovation Center in Salivary Diagnostics and Nanobiotechnology, Laboratory of Nanobiotechnology – “Luiz Ricardo Goulart”, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlândia 38496-017, Brazil (M.G.-V.)
| | - Igor Santana de Melo
- Department of Histology and Embryology, Institute of Biological Sciences and Health, Federal University of Alagoas (UFAL), Maceió 57072-260, Brazil
| | - Thúlio M. Cunha
- Department of Pulmonology, School of Medicine, Federal University of Uberlandia, Uberlândia 38496-017, Brazil
| | - Ana Carolina Gomes Jardim
- Laboratory of Antiviral Research, Department of Microbiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlândia 38496-017, Brazil
| | - Robinson Sabino-Silva
- Innovation Center in Salivary Diagnostics and Nanobiotechnology, Laboratory of Nanobiotechnology – “Luiz Ricardo Goulart”, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlândia 38496-017, Brazil (M.G.-V.)
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23
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Boys IN, Johnson AG, Quinlan MR, Kranzusch PJ, Elde NC. Structural homology screens reveal host-derived poxvirus protein families impacting inflammasome activity. Cell Rep 2023; 42:112878. [PMID: 37494187 DOI: 10.1016/j.celrep.2023.112878] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/20/2023] [Accepted: 07/11/2023] [Indexed: 07/28/2023] Open
Abstract
Viruses acquire host genes via horizontal transfer and can express them to manipulate host biology during infections. Some homologs retain sequence identity, but evolutionary divergence can obscure host origins. We use structural modeling to compare vaccinia virus proteins with metazoan proteomes. We identify vaccinia A47L as a homolog of gasdermins, the executioners of pyroptosis. An X-ray crystal structure of A47 confirms this homology, and cell-based assays reveal that A47 interferes with caspase function. We also identify vaccinia C1L as the product of a cryptic gene fusion event coupling a Bcl-2-related fold with a pyrin domain. C1 associates with components of the inflammasome, a cytosolic innate immune sensor involved in pyroptosis, yet paradoxically enhances inflammasome activity, suggesting differential modulation during infections. Our findings demonstrate the increasing power of structural homology screens to reveal proteins with unique combinations of domains that viruses capture from host genes and combine in unique ways.
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Affiliation(s)
- Ian N Boys
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Alex G Johnson
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Meghan R Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Nels C Elde
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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24
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Rabaan AA, Alwashmi ASS, Mashraqi MM, Alshehri AA, Alawfi A, Alshengeti A, Najim MA, AlShehail BM, AlShahrani AJ, Garout M. Cheminformatics and machine learning approaches for repurposing anti-viral compounds against monkeypox virus thymidylate kinase. Mol Divers 2023:10.1007/s11030-023-10705-8. [PMID: 37531040 DOI: 10.1007/s11030-023-10705-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 07/19/2023] [Indexed: 08/03/2023]
Abstract
One of the emerging epidemic concerns is Monkeypox disease which is spreading globally. This disease is caused by the monkeypox virus (MPXV), with an increasing global incidence with an outbreak in 2022. One of the novel targets for monkeypox disease is thymidylate kinase, which is involved in pyrimidine metabolism. In this study, docking-based virtual screening and molecular dynamics techniques were employed in addition to the machine learning (ML) model to investigate the potential anti-viral natural small compounds to inhibit thymidylate kinase of MPXV. Several potential hits were identified through high-throughput virtual screening, and further top three candidates were selected, which ranked using the ML model. These three compounds were then examined under molecular dynamics simulation and MM/GBSA-binding free energy analysis. Among these, Chlorhexidine HCl showed high potential for binding to the thymidylate kinase with stable and consistent conformation with RMSD < 0.3 nm. The MM/GBSA analysis also showed the minimum binding free energy (ΔGTOTAL) of -62.41 kcal/mol for this compound. Overall, this study used structure-based drug design complemented by machine learning-guided ligand-based drug design to screen potential hit compounds from the anti-viral natural compound database.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, 31311, Dhahran, Saudi Arabia.
- College of Medicine, Alfaisal University, 11533, Riyadh, Saudi Arabia.
- Department of Public Health and Nutrition, The University of Haripur, Haripur, 22610, Pakistan.
| | - Ameen S S Alwashmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, 51452, Buraydah, Saudi Arabia
| | - Mutaib M Mashraqi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, 61441, Najran, Saudi Arabia
| | - Ahmad A Alshehri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, 61441, Najran, Saudi Arabia
| | - Abdulsalam Alawfi
- Department of Pediatrics, College of Medicine, Taibah University, 41491, Medina, Saudi Arabia
| | - Amer Alshengeti
- Department of Pediatrics, College of Medicine, Taibah University, 41491, Medina, Saudi Arabia
- Department of Infection prevention and control, Prince Mohammad Bin Abdulaziz Hospital, National Guard Health Affairs, 41491, Medina, Saudi Arabia
| | - Mustafa A Najim
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Taibah University, 41411, Medina, Saudi Arabia
| | - Bashayer M AlShehail
- Pharmacy Practice Department, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Abdullah J AlShahrani
- Department of Public Health, Health affairs, Ministry of Health, 62523, Asir, Saudi Arabia
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, 21955, Mecca, Saudi Arabia.
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25
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Elhusseiny SM, Bebawy AS, Saad BT, Aboshanab KM. Insights on monkeypox disease and its recent outbreak with evidence of nonsynonymous missense mutation. Future Sci OA 2023; 9:FSO877. [PMID: 37485445 PMCID: PMC10357398 DOI: 10.2144/fsoa-2023-0048] [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: 03/16/2023] [Accepted: 06/06/2023] [Indexed: 07/25/2023] Open
Abstract
The 2022 monkeypox outbreak has created a new global health threat and pandemic. Monkeypox virus is a descendant of the genus Orthopoxvirus, producing a febrile skin rash disease in humans. Monkeypox is zoonotic transmitted and transmitted from human to human in several ways. Even though this disease is self-limited, it creates important community health worries due to its inconvenience and widespread complications. Herein, we discussed the up-to-date current situation of monkeypox regarding its epidemiology, clinical manifestations, current in-use therapeutics, necessary protective measures, and response to potential occurrences considering the recent pandemic. Also, in this review, a comparative genomic analysis of the recent circulating strains that have been recovered from various countries including, Egypt, USA, Spain, Japan and South Africa has been investigated.
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Affiliation(s)
- Shaza M Elhusseiny
- Department of Microbiology & Immunology, Faculty of Pharmacy, Ahram Canadian University (ACU), 4th Industrial Area, 6th of October City, Cairo, 12566, Egypt
| | - Abraam S Bebawy
- Department of Genomics, HITS Solutions Co., Cairo, 11765, Egypt
| | - Bishoy T Saad
- Department of Bioinformatics, HITS Solutions Co., Cairo, 11765, Egypt
| | - Khaled M Aboshanab
- Department of Microbiology & Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity St., Cairo, Abbassia, 11566, Egypt
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26
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Taouk ML, Steinig E, Taiaroa G, Savic I, Tran T, Higgins N, Tran S, Lee A, Braddick M, Moso MA, Chow EPF, Fairley CK, Towns J, Chen MY, Caly L, Lim CK, Williamson DA. Intra- and interhost genomic diversity of monkeypox virus. J Med Virol 2023; 95:e29029. [PMID: 37565686 PMCID: PMC10952654 DOI: 10.1002/jmv.29029] [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: 05/14/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/12/2023]
Abstract
The impact and frequency of infectious disease outbreaks demonstrate the need for timely genomic surveillance to inform public health responses. In the largest known outbreak of mpox, genomic surveillance efforts have primarily focused on high-incidence nations in Europe and the Americas, with a paucity of data from South-East Asia and the Western Pacific. Here we analyzed 102 monkeypox virus (MPXV) genomes sampled from 56 individuals in Melbourne, Australia. All genomes fell within the 2022 MPXV outbreak lineage (B.1), with likely onward local transmission detected. We observed within-host diversity and instances of co-infection, and highlight further examples of structural variation and apolipoprotein B editing complex-driven micro-evolution in the current MPXV outbreak. Updating our understanding of MPXV emergence and diversification will inform public health measures and enable monitoring of the virus' evolutionary trajectory throughout the mpox outbreak.
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Affiliation(s)
- Mona L. Taouk
- Department of Infectious DiseasesThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
- Victorian Infectious Diseases Reference LaboratoryThe Royal Melbourne Hospital at The Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
| | - Eike Steinig
- Department of Infectious DiseasesThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
- Victorian Infectious Diseases Reference LaboratoryThe Royal Melbourne Hospital at The Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
| | - George Taiaroa
- Department of Infectious DiseasesThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
- Victorian Infectious Diseases Reference LaboratoryThe Royal Melbourne Hospital at The Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
| | - Ivana Savic
- Victorian Infectious Diseases Reference LaboratoryThe Royal Melbourne Hospital at The Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
| | - Thomas Tran
- Victorian Infectious Diseases Reference LaboratoryThe Royal Melbourne Hospital at The Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
| | - Nasra Higgins
- Victorian Department of HealthMelbourneVictoriaAustralia
| | - Stephanie Tran
- Victorian Department of HealthMelbourneVictoriaAustralia
| | - Alvin Lee
- Victorian Department of HealthMelbourneVictoriaAustralia
| | | | - Michael A. Moso
- Department of Infectious DiseasesThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
- Victorian Infectious Diseases Reference LaboratoryThe Royal Melbourne Hospital at The Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
| | - Eric P. F. Chow
- Melbourne Sexual Health CentreAlfred HealthMelbourneVictoriaAustralia
- Central Clinical School, Faculty of Medicine, Nursing and Health SciencesMonash UniversityMelbourneVictoriaAustralia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global HealthThe University of MelbourneMelbourneVictoriaAustralia
| | - Christopher K. Fairley
- Melbourne Sexual Health CentreAlfred HealthMelbourneVictoriaAustralia
- Central Clinical School, Faculty of Medicine, Nursing and Health SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Janet Towns
- Melbourne Sexual Health CentreAlfred HealthMelbourneVictoriaAustralia
| | - Marcus Y. Chen
- Melbourne Sexual Health CentreAlfred HealthMelbourneVictoriaAustralia
| | - Leon Caly
- Department of Infectious DiseasesThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
- Victorian Infectious Diseases Reference LaboratoryThe Royal Melbourne Hospital at The Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
| | - Chuan K. Lim
- Department of Infectious DiseasesThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
- Victorian Infectious Diseases Reference LaboratoryThe Royal Melbourne Hospital at The Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
| | - Deborah A. Williamson
- Department of Infectious DiseasesThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
- Victorian Infectious Diseases Reference LaboratoryThe Royal Melbourne Hospital at The Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
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27
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Penhaskashi J, Sekimoto O, Chiappelli F. Permafrost viremia and immune tweening. Bioinformation 2023; 19:685-691. [PMID: 37885785 PMCID: PMC10598357 DOI: 10.6026/97320630019685] [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: 06/01/2023] [Revised: 06/30/2023] [Accepted: 06/30/2023] [Indexed: 10/28/2023] Open
Abstract
The immune system, an exquisitely regulated physiological system, utilizes a wide spectrum of soluble factors and multiple cell populations and subpopulations at diverse states of maturation to monitor and protect the organism against foreign organisms. Immune surveillance is ensured by distinguishing self-antigens from self-associated with non-self (e.g., viral) peptides presented by major histocompatibility complexes (MHC). Pathology is often identified as unregulated inflammatory responses (e.g., cytokine storm), or recognizing self as a non-self entity (i.e., auto-immunity). Artificial intelligence (AI), and in particular specific machine learning (ML) paradigms (e.g., Deep Learning [DL]) proffer powerful algorithms to better understand and more accurately predict immune responses, immune regulation and homeostasis, and immune reactivity to challenges (i.e., immune allostasis) by their intrinsic ability to interpret immune parameters, pathways and events by analyzing large amounts of complex data and drawing predictive inferences (i.e., immune tweening). We propose here that DL models play an increasingly significant role in better defining and characterizing immunological surveillance to ancient and novel virus species released by thawing permafrost.
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Affiliation(s)
- Jaden Penhaskashi
- />Division of West Valley Dental Implant Center, Encino, CA 91316, USA
| | | | - Francesco Chiappelli
- />Dental Group of Sherman Oaks, CA 91403 , USA
- />Center for the Health Sciences, UCLA, Los Angeles, CA, USA
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28
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Colson P, Penant G, Delerce J, Boschi C, Wurtz N, Bedotto M, Branger S, Brouqui P, Parola P, Lagier JC, Cassir N, Tissot-Dupont H, Million M, Aherfi S, La Scola B. Sequencing of monkeypox virus from infected patients reveals viral genomes with APOBEC3-like editing, gene inactivation, and bacterial agents of skin superinfection. J Med Virol 2023; 95:e28799. [PMID: 37342884 DOI: 10.1002/jmv.28799] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 04/12/2023] [Accepted: 05/08/2023] [Indexed: 06/23/2023]
Abstract
A large outbreak of Monkeypox virus (MPXV) infections has arisen in May 2022 in nonendemic countries. Here, we performed DNA metagenomics using next-generation sequencing with Illumina or Nanopore technologies for clinical samples from MPXV-infected patients diagnosed between June and July 2022. Classification of the MPXV genomes and determination of their mutational patterns were performed using Nextclade. Twenty-five samples from 25 patients were studied. A MPXV genome was obtained for 18 patients, essentially from skin lesions and rectal swabbing. All 18 genomes were classified in clade IIb, lineage B.1, and we identified four B.1 sublineages (B.1.1, B.1.10, B.1.12, B.1.14). We detected a high number of mutations (range, 64-73) relatively to a 2018 Nigerian genome (genome GenBank Accession no. NC_063383.1), which were harbored by a large part of a set of 3184 MPXV genomes of lineage B.1 recovered from GenBank and Nextstrain; and we detected 35 mutations relatively to genome ON563414.3 (a B.1 lineage reference genome). Nonsynonymous mutations occurred in genes encoding central proteins, among which transcription factors and core and envelope proteins, and included two mutations that would truncate a RNA polymerase subunit and a phospholipase d-like protein, suggesting an alternative start codon and gene inactivation, respectively. A large majority (94%) of nucleotide substitutions were G > A or C > U, suggesting the action of human APOBEC3 enzymes. Finally, >1000 reads were identified as from Staphylococcus aureus and Streptococcus pyogenes for 3 and 6 samples, respectively. These findings warrant a close genomic monitoring of MPXV to get a better picture of the genetic micro-evolution and mutational patterns of this virus, and a close clinical monitoring of skin bacterial superinfection in monkeypox patients.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Univ., Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Gwilherm Penant
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | | | - Céline Boschi
- IHU Méditerranée Infection, Marseille, France
- Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Univ., Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Nathalie Wurtz
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Marielle Bedotto
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Stéphanie Branger
- Service de Médecine Interne Infectiologie Aïgue Polyvalente, Centre hospitalier d'Avignon, Avignon, France
| | - Philippe Brouqui
- IHU Méditerranée Infection, Marseille, France
- Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Univ., Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Philippe Parola
- IHU Méditerranée Infection, Marseille, France
- Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Univ., Marseille, France
- Institut de Recherche pour le Développement (IRD), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Aix-Marseille Univ., Marseille, France
| | - Jean-Christophe Lagier
- IHU Méditerranée Infection, Marseille, France
- Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Univ., Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Nadim Cassir
- IHU Méditerranée Infection, Marseille, France
- Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Univ., Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Hervé Tissot-Dupont
- IHU Méditerranée Infection, Marseille, France
- Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Univ., Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Matthieu Million
- IHU Méditerranée Infection, Marseille, France
- Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Univ., Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Sarah Aherfi
- IHU Méditerranée Infection, Marseille, France
- Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Univ., Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, Marseille, France
- Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Univ., Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
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Elsheikh R, Makram AM, Vasanthakumaran T, Tomar S, Shamim K, Tranh ND, Elsheikh SS, Van NT, Huy NT. Monkeypox: A comprehensive review of a multifaceted virus. INFECTIOUS MEDICINE 2023; 2:74-88. [PMID: 38077831 PMCID: PMC10699692 DOI: 10.1016/j.imj.2023.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/23/2023] [Accepted: 04/29/2023] [Indexed: 03/11/2024]
Abstract
In May 2022, the world witnessed the re-emergence of the zoonotic disease monkeypox. While this was not the first epidemic of this disease, what differentiated the outbreak was the rapid global spread and increase of cases, which led the WHO to declare monkeypox a global health emergency. Although the disease spreads mainly through inadequately cooked meat of various rodent species, this virus also shows droplet, respiratory, sexual, and even vertical transmission. Monkeypox further multiplies in lymphoproliferative organs and presents with a classical smallpox-like rash, fever, headache, and muscle aches. Diagnosis is confirmed with a polymerase-chain-reaction test and is managed largely supportively with possible usage of some antivirals and immunoglobulins. Moreover, some pre-exposure and postexposure prophylactic vaccines have been developed. This paper aims to conduct an in-depth review of the historical epidemics, transmission, pathophysiology, clinical presentation, and management of the monkeypox disease.
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Affiliation(s)
- Randa Elsheikh
- Deanery of Biomedical Sciences at Edinburgh Medical School, University of Edinburgh, Edinburgh EH10 5HF, United Kingdom
- Online Research Club (http://www.onlineresearchclub.org), Nagasaki 852-8523, Japan
| | - Abdelrahman M. Makram
- Online Research Club (http://www.onlineresearchclub.org), Nagasaki 852-8523, Japan
- School of Public Health, Imperial College London, London SW7 2BX, United Kingdom
| | - Tamilarasy Vasanthakumaran
- Online Research Club (http://www.onlineresearchclub.org), Nagasaki 852-8523, Japan
- Global Clinical Scholars Research Training, Harvard Medical School, Boston, MA 02115, USA
| | | | | | - Nguyen Dong Tranh
- Online Research Club (http://www.onlineresearchclub.org), Nagasaki 852-8523, Japan
- Department of Infection Control, Binh Dinh Provincial General Hospital, Binh Dinh 55000, Vietnam
| | | | - Nguyen Thanh Van
- Online Research Club (http://www.onlineresearchclub.org), Nagasaki 852-8523, Japan
- Global Clinical Scholars Research Training, Harvard Medical School, Boston, MA 02115, USA
| | - Nguyen Tien Huy
- Online Research Club (http://www.onlineresearchclub.org), Nagasaki 852-8523, Japan
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki 852-8523, Japan
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30
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Brinkmann A, Kohl C, Pape K, Bourquain D, Thürmer A, Michel J, Schaade L, Nitsche A. Extensive ITR expansion of the 2022 Mpox virus genome through gene duplication and gene loss. Virus Genes 2023:10.1007/s11262-023-02002-1. [PMID: 37256469 DOI: 10.1007/s11262-023-02002-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/29/2023] [Indexed: 06/01/2023]
Abstract
Poxviruses are known to evolve slower than RNA viruses with only 1-2 mutations/genome/year. Rather than single mutations, rearrangements such as gene gain and loss, which have been discussed as a possible driver for host adaption, were described in poxviruses. In 2022 and 2023 the world is being challenged by the largest global outbreak so far of Mpox virus, and the virus seems to have established itself in the human community for an extended period of time. Here, we report five Mpox virus genomes from Germany with extensive gene duplication and loss, leading to the expansion of the ITR regions from 6400 to up to 24,600 bp. We describe duplications of up to 18,200 bp to the opposed genome end, and deletions at the site of insertion of up to 16,900 bp. Deletions and duplications of genes with functions of supposed immune modulation, virulence and host adaption as B19R, B21R, B22R and D10L are described. In summary, we highlight the need for monitoring rearrangements of the Mpox virus genome rather than for monitoring single mutations only.
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Affiliation(s)
- Annika Brinkmann
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany.
| | - Claudia Kohl
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Katharina Pape
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Daniel Bourquain
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Andrea Thürmer
- Genome Sequencing and Genomic Epidemiology, Methodology and Research Infrastructure, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Janine Michel
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Lars Schaade
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
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31
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Sahu A, Gaur M, Mahanandia NC, Subudhi E, Swain RP, Subudhi BB. Identification of core therapeutic targets for Monkeypox virus and repurposing potential of drugs against them: An in silico approach. Comput Biol Med 2023; 161:106971. [PMID: 37211001 DOI: 10.1016/j.compbiomed.2023.106971] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 04/11/2023] [Accepted: 04/19/2023] [Indexed: 05/23/2023]
Abstract
Monkeypox virus (mpox virus) outbreak has rapidly spread to 82 non-endemic countries. Although it primarily causes skin lesions, secondary complications and high mortality (1-10%) in vulnerable populations have made it an emerging threat. Since there is no specific vaccine/antiviral, it is desirable to repurpose existing drugs against mpox virus. With little knowledge about the lifecycle of mpox virus, identifying potential inhibitors is a challenge. Nevertheless, the available genomes of mpox virus in public databases represent a goldmine of untapped possibilities to identify druggable targets for the structure-based identification of inhibitors. Leveraging this resource, we combined genomics and subtractive proteomics to identify highly druggable core proteins of mpox virus. This was followed by virtual screening to identify inhibitors with affinities for multiple targets. 125 publicly available genomes of mpox virus were mined to identify 69 highly conserved proteins. These proteins were then curated manually. These curated proteins were funnelled through a subtractive proteomics pipeline to identify 4 highly druggable, non-host homologous targets namely; A20R, I7L, Top1B and VETFS. High-throughput virtual screening of 5893 highly curated approved/investigational drugs led to the identification of common as well as unique potential inhibitors with high binding affinities. The common inhibitors, i.e., batefenterol, burixafor and eluxadoline were further validated by molecular dynamics simulation to identify their best potential binding modes. The affinity of these inhibitors suggests their repurposing potential. This work can encourage further experimental validation for possible therapeutic management of mpox.
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Affiliation(s)
- Anshuman Sahu
- Drug Development and Analysis Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, 751030, India
| | - Mahendra Gaur
- Drug Development and Analysis Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, 751030, India; Department of Biotechnology, Punjabi University, Patiala, 147002, India
| | - Nimai Charan Mahanandia
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Pusa, New Delhi, 110012, India
| | - Enketeswara Subudhi
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, 751030, India
| | - Ranjit Prasad Swain
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, 751030, India
| | - Bharat Bhusan Subudhi
- Drug Development and Analysis Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, 751030, India.
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Crespo-Bellido A, Duffy S. The how of counter-defense: viral evolution to combat host immunity. Curr Opin Microbiol 2023; 74:102320. [PMID: 37075547 DOI: 10.1016/j.mib.2023.102320] [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: 01/07/2023] [Revised: 03/10/2023] [Accepted: 03/23/2023] [Indexed: 04/21/2023]
Abstract
Viruses are locked in an evolutionary arms race with their hosts. What ultimately determines viral evolvability, or capacity for adaptive evolution, is their ability to efficiently explore and expand sequence space while under the selective regime imposed by their ecology, which includes innate and adaptive host defenses. Viral genomes have significantly higher evolutionary rates than their host counterparts and should have advantages relative to their slower-evolving hosts. However, functional constraints on virus evolutionary landscapes along with the modularity and mutational tolerance of host defense proteins may help offset the advantage conferred to viruses by high evolutionary rates. Additionally, cellular life forms from all domains of life possess many highly complex defense mechanisms that act as hurdles to viral replication. Consequently, viruses constantly probe sequence space through mutation and genetic exchange and are under pressure to optimize diverse counter-defense strategies.
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Affiliation(s)
- Alvin Crespo-Bellido
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA.
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33
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Boys IN, Johnson AG, Quinlan M, Kranzusch PJ, Elde NC. Structural homology screens reveal poxvirus-encoded proteins impacting inflammasome-mediated defenses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.26.529821. [PMID: 36909515 PMCID: PMC10002665 DOI: 10.1101/2023.02.26.529821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Viruses acquire host genes via horizontal gene transfer and can express them to manipulate host biology during infections. Some viral and host homologs retain sequence identity, but evolutionary divergence can obscure host origins. We used structural modeling to compare vaccinia virus proteins with metazoan proteomes. We identified vaccinia A47L as a homolog of gasdermins, the executioners of pyroptosis. An X-ray crystal structure of A47 confirmed this homology and cell-based assays revealed that A47 inhibits pyroptosis. We also identified vaccinia C1L as the product of a cryptic gene fusion event coupling a Bcl-2 related fold with a pyrin domain. C1 associates with components of the inflammasome, a cytosolic innate immune sensor involved in pyroptosis, yet paradoxically enhances inflammasome activity, suggesting a benefit to poxvirus replication in some circumstances. Our findings demonstrate the potential of structural homology screens to reveal genes that viruses capture from hosts and repurpose to benefit viral fitness.
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Affiliation(s)
- Ian N. Boys
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, 84112 USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, 20815, USA
| | - Alex G. Johnson
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Meghan Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, 84112 USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, 20815, USA
| | - Philip J. Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Nels C. Elde
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, 84112 USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, 20815, USA
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34
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Taha TY, Townsend MB, Pohl J, Karem KL, Damon IK, Mbala Kingebeni P, Muyembe Tamfum JJ, Martin JW, Pittman PR, Huggins JW, Satheshkumar PS, Bagarozzi DA, Reynolds MG, Hughes LJ. Design and Optimization of a Monkeypox virus Specific Serological Assay. Pathogens 2023; 12:pathogens12030396. [PMID: 36986317 PMCID: PMC10054672 DOI: 10.3390/pathogens12030396] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/05/2023] Open
Abstract
Monkeypox virus (MPXV), a member of the Orthopoxvirus (OPXV) genus, is a zoonotic virus, endemic to central and western Africa that can cause smallpox-like symptoms in humans with fatal outcomes in up to 15% of patients. The incidence of MPXV infections in the Democratic Republic of the Congo, where the majority of cases have occurred historically, has been estimated to have increased as much as 20-fold since the end of smallpox vaccination in 1980. Considering the risk global travel carries for future disease outbreaks, accurate epidemiological surveillance of MPXV is warranted as demonstrated by the recent Mpox outbreak, where the majority of cases were occurring in non-endemic areas. Serological differentiation between childhood vaccination and recent infection with MPXV or other OPXVs is difficult due to the high level of conservation within OPXV proteins. Here, a peptide-based serological assay was developed to specifically detect exposure to MPXV. A comparative analysis of immunogenic proteins across human OPXVs identified a large subset of proteins that could potentially be specifically recognized in response to a MPXV infection. Peptides were chosen based upon MPXV sequence specificity and predicted immunogenicity. Peptides individually and combined were screened in an ELISA against serum from well-characterized Mpox outbreaks, vaccinee sera, and smallpox sera collected prior to eradication. One peptide combination was successful with ~86% sensitivity and ~90% specificity. The performance of the assay was assessed against the OPXV IgG ELISA in the context of a serosurvey by retrospectively screening a set of serum specimens from the region in Ghana believed to have harbored the MPXV-infected rodents involved in the 2003 United States outbreak.
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Affiliation(s)
- Taha Y. Taha
- Reagent and Diagnostic Services Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Michael B. Townsend
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Jan Pohl
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Kevin L. Karem
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Inger K. Damon
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Placide Mbala Kingebeni
- Institut National de Recherche Biomédicale, Ministère de la Santé Publique, Kinshasa P.O. Box 1197, Democratic Republic of the Congo
| | - Jean-Jacques Muyembe Tamfum
- Institut National de Recherche Biomédicale, Ministère de la Santé Publique, Kinshasa P.O. Box 1197, Democratic Republic of the Congo
| | - James W. Martin
- Department of Clinical Research, Division of Medicine, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, MD 21702, USA
| | - Phillip R. Pittman
- Department of Clinical Research, Division of Medicine, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, MD 21702, USA
| | - John W. Huggins
- Department of Clinical Research, Division of Medicine, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, MD 21702, USA
| | - Panayampalli S. Satheshkumar
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Dennis A. Bagarozzi
- Reagent and Diagnostic Services Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Mary G. Reynolds
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Laura J. Hughes
- Reagent and Diagnostic Services Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
- Correspondence:
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35
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Brennan G, Stoian AMM, Yu H, Rahman MJ, Banerjee S, Stroup JN, Park C, Tazi L, Rothenburg S. Molecular Mechanisms of Poxvirus Evolution. mBio 2023; 14:e0152622. [PMID: 36515529 PMCID: PMC9973261 DOI: 10.1128/mbio.01526-22] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Poxviruses are often thought to evolve relatively slowly because they are double-stranded DNA pathogens with proofreading polymerases. However, poxviruses have highly adaptable genomes and can undergo relatively rapid genotypic and phenotypic change, as illustrated by the recent increase in human-to-human transmission of monkeypox virus. Advances in deep sequencing technologies have demonstrated standing nucleotide variation in poxvirus populations, which has been underappreciated. There is also an emerging understanding of the role genomic architectural changes play in shaping poxvirus evolution. These mechanisms include homologous and nonhomologous recombination, gene duplications, gene loss, and the acquisition of new genes through horizontal gene transfer. In this review, we discuss these evolutionary mechanisms and their potential roles for adaption to novel host species and modulating virulence.
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Affiliation(s)
- Greg Brennan
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - Ana M. M. Stoian
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - Huibin Yu
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - M. Julhasur Rahman
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - Shefali Banerjee
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - Jeannine N. Stroup
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - Chorong Park
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - Loubna Tazi
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - Stefan Rothenburg
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
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36
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Americo JL, Earl PL, Moss B. Virulence differences of mpox (monkeypox) virus clades I, IIa, and IIb.1 in a small animal model. Proc Natl Acad Sci U S A 2023; 120:e2220415120. [PMID: 36787354 PMCID: PMC9974501 DOI: 10.1073/pnas.2220415120] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/19/2023] [Indexed: 02/15/2023] Open
Abstract
Human mpox (monkeypox), a disease with similarities to smallpox, is endemic in Africa where it has persisted as a zoonosis with limited human-to-human spread. Unexpectedly, the disease expanded globally in 2022 driven by human-to-human transmission outside of Africa. It is not yet known whether the latter is due solely to behavioral and environmental factors or whether the mpox virus is adapting to a new host. Genome sequencing has revealed differences between the current outbreak strains, classified as clade IIb, and the prior clade IIa and clade I viruses, but whether these differences contribute to virulence or transmission has not been determined. We demonstrate that the wild-derived inbred castaneous mouse provides an exceptional animal model for investigating clade differences in mpox virus virulence and show that the order is clade I > clade IIa > clade IIb.1. The greatly reduced replication of the clade IIb.1 major outbreak strain in mice and absence of lethality at 100 times the lethal dose of a closely related clade IIa virus, despite similar multiplication in cell culture, suggest that clade IIb is evolving diminished virulence or adapting to other species.
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Affiliation(s)
- Jeffrey L. Americo
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20814
| | - Patricia L. Earl
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20814
| | - Bernard Moss
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20814
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37
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Cowpox Viruses: A Zoo Full of Viral Diversity and Lurking Threats. Biomolecules 2023; 13:biom13020325. [PMID: 36830694 PMCID: PMC9953750 DOI: 10.3390/biom13020325] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
Cowpox viruses (CPXVs) exhibit the broadest known host range among the Poxviridae family and have caused lethal outbreaks in various zoo animals and pets across 12 Eurasian countries, as well as an increasing number of human cases. Herein, we review the history of how the cowpox name has evolved since the 1700s up to modern times. Despite early documentation of the different properties of CPXV isolates, only modern genetic analyses and phylogenies have revealed the existence of multiple Orthopoxvirus species that are currently constrained under the CPXV designation. We further chronicle modern outbreaks in zoos, domesticated animals, and humans, and describe animal models of experimental CPXV infections and how these can help shaping CPXV species distinctions. We also describe the pathogenesis of modern CPXV infections in animals and humans, the geographic range of CPXVs, and discuss CPXV-host interactions at the molecular level and their effects on pathogenicity and host range. Finally, we discuss the potential threat of these viruses and the future of CPXV research to provide a comprehensive review of CPXVs.
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38
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Forni D, Moltrasio C, Sironi M, Mozzi A, Quattri E, Venegoni L, Zamprogno M, Citterio A, Clerici M, Marzano AV, Cagliani R. Whole-genome sequencing of hMPXV1 in five Italian cases confirms the occurrence of the predominant epidemic lineage. J Med Virol 2023; 95:e28493. [PMID: 36633196 PMCID: PMC10108130 DOI: 10.1002/jmv.28493] [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: 12/06/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/13/2023]
Abstract
The ongoing outbreak of monkeypox virus (hMPXV1) is the largest recorded in historically nonendemic countries. Genomic surveillance has emerged as a pivotal tool to track the spread and monitor the evolution of viral pathogens. Therefore, to assess the genetic diversity of circulating hMPXV1 in northern Italy in June to July 2022, we sequenced and analyzed five complete genomes of viruses sampled from patients presenting with a typical course of hMPXV1 infection. Phylogenetic analysis confirmed that all five genomes belong to the predominant epidemic lineage (B.1). Inspection of genetic changes and comparison with the reference sequence showed the presence of 12 nucleotide substitutions. Seven are nonsynonymous mutations leading to amino acid changes in six proteins belonging to different functional classes. Moreover, 11 of these 12 nucleotide mutations involve GA>AA or TC>TT replacements, suggesting that host APOBEC3 enzymes are responsible for the generation of substitutions in circulating viruses. Finally, metagenomic analysis evidenced bacterial superinfection (Streptococcus pyogenes) in one patient. Through this study, we contributed to expand the number of complete genomes of viruses circulating in Italy and characterize them as belonging to the predominant outbreak lineage.
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Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Chiara Moltrasio
- Dermatology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Alessandra Mozzi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Eleonora Quattri
- Dermatology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.,Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Luigia Venegoni
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Marzia Zamprogno
- Dermatology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Andrea Citterio
- Laboratory of Molecular Biology, Scientific Institute IRCCS E. MEDEA, Bosisio Parini, Italy
| | - Mario Clerici
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.,Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Angelo Valerio Marzano
- Dermatology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.,Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
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39
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Galán-Huerta KA, Paz-Infanzon M, Nuzzolo-Shihadeh L, Ruiz-Higareda AF, Bocanegra-Ibarias P, Villareal-Martínez DZ, Muñoz-Garza FZ, Guerrero-Putz MD, Sáenz-Ibarra B, Barboza-Quintana O, Ocampo-Candiani J, Rivas-Estilla AM, Camacho-Ortiz A. Metagenomic Sequencing of Monkeypox Virus, Northern Mexico. Emerg Infect Dis 2023; 29:448-450. [PMID: 36648111 PMCID: PMC9881790 DOI: 10.3201/eid2902.221199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Monkeypox virus (MPXV) has gained interest because of a multicountry outbreak of mpox (formerly monkeypox) cases with no epidemiologic link to MPXV-endemic regions. We sequenced the complete genome of MPXV isolated from a patient in northern Mexico. Phylogenetic analysis grouped the virus with isolates from Germany.
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Molteni C, Forni D, Cagliani R, Mozzi A, Clerici M, Sironi M. Evolution of the orthopoxvirus core genome. Virus Res 2023; 323:198975. [PMID: 36280003 PMCID: PMC9586335 DOI: 10.1016/j.virusres.2022.198975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/07/2022]
Abstract
Orthopoxviruses comprise several relevant pathogens, including the causative agent of smallpox and monkeypox virus. Analysis of orthopoxvirus genome evolution mainly focused on gene gains/losses. We instead analyzed core genes, which are conserved in all orthopoxviruses. We show that, despite their strong constraint, some genes involved in viral morphogenesis and transcription/replication were targets of pervasive positive selection, which was relatively uncommon in immunomodulatory genes. However at least three of the positively selected genes, E3L, A24R, and H3L, might have evolved in response to immune selection. Episodic positive selection was particularly common on the internal branches of the orthopox phylogeny and on the monkeypox virus lineage. The latter showed evidence of episodic positive selection at the D14L gene, which encodes a modulator of complement activation (MOPICE). Notably, two genes (B1R and A33R) targeted by episodic selection on more than one branch are involved in forms of intra-genomic conflict. Finally, we found that, in orthopoxvirus proteomes, intrinsically disordered regions (IDRs) tend to be less constrained and are common targets of positive selection. Extension of our analysis to all poxviruses showed no evidence that the IDR fraction differs with host range. Conversely, we found a strong effect of base composition, which was however not sufficient to explain IDR fraction. We thus suggest that, in poxviruses, the IDR fraction is maintained by modulating GC content to accommodate disorder-promoting codons. Overall, our data provide novel insight in orthopoxvirus evolution and provide a list of genes and sites that are expected to modulate viral phenotypes.
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Affiliation(s)
- Cristian Molteni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy.
| | - Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Alessandra Mozzi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Mario Clerici
- University of Milan, Milan, Italy; Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
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Sharma R, Chen KT, Sharma R. Emerging evidence on Monkeypox: resurgence, global burden, molecular insights, genomics and possible management. Front Cell Infect Microbiol 2023; 13:1134712. [PMID: 37153147 PMCID: PMC10154632 DOI: 10.3389/fcimb.2023.1134712] [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: 12/30/2022] [Accepted: 02/20/2023] [Indexed: 05/09/2023] Open
Abstract
An outbreak of monkeypox (encoded enveloped double stranded DNA), resurgence and expansion has emerged in early 2022, posing a new threat to global health. Even though, many reports are available on monkeypox, still a comprehensive updated review is needed. Present updated review is focused to fill the research gaps pertaining to the monkeypox, and an extensive search was conducted in a number of databases, including Google Scholar, Scopus, Web of Science, and Science Direct. Although the disease usually progresses self-limiting, some patients require admission for kidney injury, pharyngitis, myocarditis, and soft tissue super infections. There is no well-known treatment available yet; still there has been a push for the use of antiviral therapy and tecovirimat as a promising option when dealing with co-morbidities. In this study, we mapped and discussed the updates and scientific developments surrounding monkeypox, including its potential molecular mechanisms, genomics, transmission, risk factors, diagnosis, prevention, vaccines, treatment, possible plant-based treatment along with their proposed mechanisms. Each day, a growing number of monkeypox cases are reported, and more cases are expected in the near future. As of now, monkeypox does not have a well-established and proven treatment, and several investigations are underway to find the best possible treatment from natural or synthetic drug sources. Multiple molecular mechanisms on pathophysiological cascades of monkeypox virus infection are discussed here along with updates on genomics, and possible preventive and therapeutic strategies.
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Affiliation(s)
- Ruchi Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, India
| | - Kow-Tong Chen
- Department of Occupational Medicine, Tainan Municipal Hospital (managed by Show Chwan Medical Care Corporation), Tainan, Taiwan
- Department of Public Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- *Correspondence: Rohit Sharma, ; Kow-Tong Chen,
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, India
- *Correspondence: Rohit Sharma, ; Kow-Tong Chen,
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What Do We Know About the Smallpox Virus? A Journey Between Clinic and Therapy. Pharm Res 2023; 40:459-465. [PMID: 36451069 PMCID: PMC9713125 DOI: 10.1007/s11095-022-03447-z] [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: 10/17/2022] [Accepted: 11/22/2022] [Indexed: 12/04/2022]
Abstract
PURPOSE Modern research is increasingly focusing on the study of new viruses and the re-emergence of past microbes, such as Coronaviruses, particularly Sars-Cov2 that was responsible for the very recent pandemic. METHODS AND RESULTS This infection manifested itself and still continues to manifest as a severe respiratory syndrome. The main discriminator of whether or not one succeeds in overcoming this infection may depend on a great many factors, but the main one is definitely determined by vaccination, which has minimized hospitalizations and more severe syndromes. CONCLUSION Recently, a new virus, the monkeypox virus, which was previously confined to Central and West Africa but is now gradually spreading to more than 30 countries including the United States of America, where such an infection is not endemic, is coming forward again.
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Mukherjee AG, Wanjari UR, Kannampuzha S, Das S, Murali R, Namachivayam A, Renu K, Ramanathan G, Doss C GP, Vellingiri B, Dey A, Valsala Gopalakrishnan A. The pathophysiological and immunological background of the monkeypox virus infection: An update. J Med Virol 2023; 95:e28206. [PMID: 36217803 DOI: 10.1002/jmv.28206] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 01/18/2023]
Abstract
In addition to the COVID-19 waves, the globe is facing global monkeypox (MPX) outbreak. MPX is an uncommon zoonotic infection characterized by symptoms similar to smallpox. It is caused by the monkeypox virus (MPXV), a double-stranded DNA virus that belongs to the genus Orthopoxvirus (OPXV). MPXV, which causes human disease, has been confined to Africa for many years, with only a few isolated cases in other areas. Outside of Africa, the continuing MPXV outbreak in multiple countries in 2022 is the greatest in recorded history. The current outbreak, with over 10 000 confirmed cases in over 50 countries between May and July 2022, demonstrates that MPXV may travel rapidly among humans and pose a danger to human health worldwide. The rapid spread of such outbreaks in recent times has elevated MPX to the status of a rising zoonotic disease with significant epidemic potential. While the MPXV is not as deadly or contagious as the variola virus that causes smallpox, it poses a threat because it could evolve into a more potent human pathogen. This review assesses the potential threat to the human population and provides a brief overview of what is currently known about this reemerging virus. By analyzing the biological effects of MPXV on human health, its shifting epidemiological footprint, and currently available therapeutic options, this review has presented the most recent insights into the biology of the virus. This study also clarifies the key potential causes that could be to blame for the present MPX outbreak and draw attention to major research questions and promising new avenues for combating the current MPX epidemic.
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Affiliation(s)
- Anirban Goutam Mukherjee
- Department of Biomedical Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Uddesh Ramesh Wanjari
- Department of Biomedical Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Sandra Kannampuzha
- Department of Biomedical Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Soumik Das
- Department of Biomedical Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Reshma Murali
- Department of Biomedical Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Arunraj Namachivayam
- Department of Biomedical Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Kaviyarasi Renu
- Department of Biochemistry, Centre of Molecular Medicine and Diagnostics (COMManD), Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Gnanasambandan Ramanathan
- Department of Biomedical Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - George Priya Doss C
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Balachandar Vellingiri
- Department of Human Genetics and Molecular Biology, Human Molecular Cytogenetics and Stem Cell Laboratory, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
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Shete AM, Yadav PD, Kumar A, Patil S, Patil DY, Joshi Y, Majumdar T, Relhan V, Sahay RR, Vasu M, Gawande P, Verma A, Kumar A, Dhakad S, Krishnan AB, Chenayil S, Kumar S, Abraham P. Genome characterization of monkeypox cases detected in India: Identification of three sub clusters among A.2 lineage. J Infect 2023; 86:66-117. [PMID: 36179885 PMCID: PMC9534117 DOI: 10.1016/j.jinf.2022.09.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 02/04/2023]
Affiliation(s)
- Anita M. Shete
- Maximum Containment Facility, National Institute of Virology, Indian Council of Medical Research-National Institute of Virology, Sus Road, Pashan, Pune, Maharashtra 411021, India
| | - Pragya D. Yadav
- Maximum Containment Facility, National Institute of Virology, Indian Council of Medical Research-National Institute of Virology, Sus Road, Pashan, Pune, Maharashtra 411021, India,Corresponding author
| | - Abhinendra Kumar
- Maximum Containment Facility, National Institute of Virology, Indian Council of Medical Research-National Institute of Virology, Sus Road, Pashan, Pune, Maharashtra 411021, India
| | - Savita Patil
- Maximum Containment Facility, National Institute of Virology, Indian Council of Medical Research-National Institute of Virology, Sus Road, Pashan, Pune, Maharashtra 411021, India
| | - Deepak Y. Patil
- Maximum Containment Facility, National Institute of Virology, Indian Council of Medical Research-National Institute of Virology, Sus Road, Pashan, Pune, Maharashtra 411021, India
| | - Yash Joshi
- Maximum Containment Facility, National Institute of Virology, Indian Council of Medical Research-National Institute of Virology, Sus Road, Pashan, Pune, Maharashtra 411021, India
| | - Triparna Majumdar
- Maximum Containment Facility, National Institute of Virology, Indian Council of Medical Research-National Institute of Virology, Sus Road, Pashan, Pune, Maharashtra 411021, India
| | - Vineet Relhan
- Maulana Azad Medical College and Lok Nayak Hospital, New Delhi 110002, India
| | - Rima R. Sahay
- Maximum Containment Facility, National Institute of Virology, Indian Council of Medical Research-National Institute of Virology, Sus Road, Pashan, Pune, Maharashtra 411021, India
| | - Meenakshy Vasu
- Public Health Department of Kerala, Directorate of Health Services, Thiruvananthapuram 695035, India
| | - Pranita Gawande
- Maximum Containment Facility, National Institute of Virology, Indian Council of Medical Research-National Institute of Virology, Sus Road, Pashan, Pune, Maharashtra 411021, India
| | - Ajay Verma
- Maximum Containment Facility, National Institute of Virology, Indian Council of Medical Research-National Institute of Virology, Sus Road, Pashan, Pune, Maharashtra 411021, India
| | - Arbind Kumar
- All India Institute of Medical Sciences, New Delhi 110029, India
| | - Shivram Dhakad
- All India Institute of Medical Sciences, New Delhi 110029, India
| | - Anukumar Bala Krishnan
- Indian Council of Medical Research-National Institute of Virology, Alappuzha, Kerala 688005, India
| | - Shubin Chenayil
- State Surveillance Unit (IDSP), Directorate of Health Services (IDSP), Malappuram, Kerala 688005, India
| | - Suresh Kumar
- Maulana Azad Medical College and Lok Nayak Hospital, New Delhi 110002, India
| | - Priya Abraham
- Maximum Containment Facility, National Institute of Virology, Indian Council of Medical Research-National Institute of Virology, Sus Road, Pashan, Pune, Maharashtra 411021, India
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Paniz-Mondolfi A, Guerra S, Muñoz M, Luna N, Hernandez MM, Patino LH, Reidy J, Banu R, Shrestha P, Liggayu B, Umeaku A, Chen F, Cao L, Patel A, Hanna A, Li S, Look A, Pagani N, Albrecht R, Pearl R, Garcia-Sastre A, Bogunovic D, Palacios G, Bonnier L, Cera F, Lopez H, Calderon Y, Eiting E, Mullen K, Shin SJ, Lugo LA, Urbina AE, Starks C, Koo T, Uychiat P, Look A, van Bakel H, Gonzalez-Reiche A, Betancourt AF, Reich D, Cordon-Cardo C, Simon V, Sordillo EM, Ramírez JD. Evaluation and validation of an RT-PCR assay for specific detection of monkeypox virus (MPXV). J Med Virol 2023; 95:e28247. [PMID: 36271493 DOI: 10.1002/jmv.28247] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/11/2022] [Accepted: 10/19/2022] [Indexed: 01/11/2023]
Abstract
Monkeypox virus (MPXV) is a zoonotic orthopoxvirus within the Poxviridae family. MPXV is endemic to Central and West Africa. However, the world is currently witnessing an international outbreak with no clear epidemiological links to travel or animal exposure and with ever-increasing numbers of reported cases worldwide. Here, we evaluated and validated a new, sensitive, and specific real-time PCR-assay for MPXV diagnosis in humans and compare the performance of this novel assay against a Food & Drug Administration-cleared pan-Orthopox RT-PCR assay. We determined specificity, sensitivity, and analytic performance of the PKamp™ Monkeypox Virus RT-PCR assay targeting the viral F3L-gene. In addition, we further evaluated MPXV-PCR-positive specimens by viral culture, electron microscopy, and viral inactivation assays. The limit of detection was established at 7.2 genome copies/reaction, and MPXV was successfully identified in 20 clinical specimens with 100% correlation against the reference method with 100% sensitivity and specificity. Our results demonstrated the validity of this rapid, robust, and reliable RT-PCR assay for specific and accurate diagnosis of MPXV infection in human specimens collected both as dry swabs and in viral transport media. This assay has been approved by NYS Department of Health for clinical use.
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Affiliation(s)
- Alberto Paniz-Mondolfi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Susana Guerra
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Nicolas Luna
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Matthew M Hernandez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Luz H Patino
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jason Reidy
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Radhika Banu
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Paras Shrestha
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Bernadette Liggayu
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Audrey Umeaku
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Feng Chen
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Liyong Cao
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Armi Patel
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ayman Hanna
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sunny Li
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Andy Look
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nina Pagani
- Department of Biotechnology Laboratory Sciences, Valencia College, Orlando, Florida, USA.,Infectious Diseases Research Branch, Venezuelan Science Incubator and The Zoonosis and Emerging Pathogens Regional Collaborative Network, Cabudare, Lara, Venezuela
| | - Randy Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Rebecca Pearl
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Adolfo Garcia-Sastre
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Dusan Bogunovic
- Department of Microbiology, Center for Inborn Errors of Immunity, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Gustavo Palacios
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lucia Bonnier
- Department of Pathology and Laboratory Medicine, Mount Sinai Beth Israel, New York, New York, USA
| | - Freddy Cera
- Department of Pathology and Laboratory Medicine, Mount Sinai Beth Israel, New York, New York, USA
| | - Heidi Lopez
- Department of Pathology and Laboratory Medicine, Mount Sinai Beth Israel, New York, New York, USA
| | - Yvette Calderon
- Department of Emergency Medicine, Mount Sinai Beth Israel, New York, New York, USA
| | - Erick Eiting
- Department of Emergency Medicine, Mount Sinai Beth Israel, New York, New York, USA
| | - Karr Mullen
- Department of Emergency Medicine, Mount Sinai Beth Israel, New York, New York, USA
| | - Sangyoon Jason Shin
- Department of Medicine, Ambulatory Care, The Center for Transgender Medicine and Surgery (CTMS) of Mount Sinai, Mount Sinai Beth Israel, New York, New York, USA
| | - Luz Amarilis Lugo
- Division of Infectious Diseases, Institute for Advanced Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Antonio E Urbina
- Division of Infectious Diseases, Institute for Advanced Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Carlotta Starks
- Mount Sinai Institute for Advanced Medicine, Jack Martin Fund Clinic and Comprehensive Health Clinic, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Tonny Koo
- Laboratory of Medical Microbiology, Mount Sinai Hospital, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Patricia Uychiat
- Department of Pathology and Laboratory Medicine, Mount Sinai West, New York, New York, USA
| | - Avery Look
- Cornell University College of Agriculture and Life Sciences, Ithaca, New York, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ana Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Adolfo Firpo Betancourt
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David Reich
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Viviana Simon
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Emilia M Sordillo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Juan David Ramírez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
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46
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Pharmacological Agents with Antiviral Activity against Monkeypox Infection. Int J Mol Sci 2022; 23:ijms232415941. [PMID: 36555584 PMCID: PMC9784635 DOI: 10.3390/ijms232415941] [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: 11/21/2022] [Revised: 12/06/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022] Open
Abstract
Monkeypox infection is caused by a virus of the genus Orthopoxvirus, a member of the Poxviridae family. Monkeypox virus is transmitted from individual to individual through contact with lesions, body fluids, and respiratory droplets. The infection caused by monkeypox is usually a self-limited disease with mild symptoms lasting 2 to 4 weeks. Monkeypox typically presents with fever, rash, and enlarged lymph nodes. New vaccines have recently been authorized for the prevention of monkeypox infection, whereas there are no specific pharmacological antiviral treatments for monkeypox infection. However, because the viruses which cause adult smallpox and monkeypox are similar, antiviral drugs developed in the past have also shown efficacy against monkeypox. In this review, we highlight the in vitro and clinical evidence found in the literature on the efficacy and safety of pharmacological agents with antiviral activity against monkeypox infection and the different regulatory aspects of countries.
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47
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Xiang Y, White A. Monkeypox virus emerges from the shadow of its more infamous cousin: family biology matters. Emerg Microbes Infect 2022; 11:1768-1777. [PMID: 35751396 PMCID: PMC9278444 DOI: 10.1080/22221751.2022.2095309] [Citation(s) in RCA: 82] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/23/2022] [Accepted: 06/23/2022] [Indexed: 11/25/2022]
Abstract
Monkeypox virus (MPXV) is closely related to the infamous variola (smallpox) virus, causing a febrile rash illness in humans similar to but milder than smallpox. In the twentieth century, human monkeypox had been mostly a rare zoonotic disease confined to forested areas in West and Central Africa. However, the case number and geographic range have increased significantly in this century, coincided with the waning of the smallpox vaccine-induced immunity in the global population. The outbreak of human monkeypox in multiple countries since May 2022 has been unusual in its large case number and the absence of direct links to endemic countries, raising concerns for a possible change in monkeypox transmission pattern that could pose a greater global threat. Here, we review aspects of MPXV biology that are relevant for risk assessment and preparedness for a monkeypox epidemic, with an emphasis on recent progress in understanding of the virus host range, evolutionary potential, and neutralization targets.
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Affiliation(s)
- Yan Xiang
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center, San Antonio, TX, USA
| | - Addison White
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center, San Antonio, TX, USA
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Rahman MM, McFadden G. Role of cytokines in poxvirus host tropism and adaptation. Curr Opin Virol 2022; 57:101286. [PMID: 36427482 PMCID: PMC9704024 DOI: 10.1016/j.coviro.2022.101286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/19/2022] [Accepted: 10/26/2022] [Indexed: 11/23/2022]
Abstract
Poxviruses are a diverse family of double-stranded DNA viruses that cause mild-to-severe disease in selective hosts, including humans. Although most poxviruses are restricted to their hosts, some members can leap host species and cause zoonotic diseases and, therefore, are genuine threats to human and animal health. The recent global spread of monkeypox in humans suggests that zoonotic poxviruses can adapt to a new host, spread rapidly in the new host, and evolve to better evade host innate barriers. Unlike many other viruses, poxviruses express an extensive repertoire of self-defense proteins that play a vital role in the evasion of host innate and adaptive immune responses in their newest host species. The function of these viral immune modulators and host-specific cytokine responses can result in different host tropism and poxvirus disease progression. Here, we review the role of different cytokines that control poxvirus host tropism and adaptation.
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Johri N, Kumar D, Nagar P, Maurya A, Vengat M, Jain P. Clinical manifestations of human monkeypox infection and implications for outbreak strategy. HEALTH SCIENCES REVIEW (OXFORD, ENGLAND) 2022; 5:100055. [PMID: 36254190 PMCID: PMC9535997 DOI: 10.1016/j.hsr.2022.100055] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/08/2022] [Accepted: 10/02/2022] [Indexed: 11/09/2022]
Abstract
Monkeypox is an orthopoxvirus-based zoonotic illness that causes symptoms similar to smallpox in humans. Health care workers around the world are making it a priority to educate themselves on the many clinical manifestations and treatment options for this virus as public health agencies strive to stop the current outbreak. The infected do not have access to any treatment at this time. However, information obtained from the smallpox pandemic has led researchers to examine vaccinia immune globulin (IVG), tecovirimat, and cidofovir as viable treatments for monkeypox. Moreover, medication like tecovirimat may be given in extreme circumstances, and supportive therapy can help with symptom relief. The European Medicines Agency (EMA) certified tecovirimat as safe and effective against monkeypox in 2022, per the World Health Organization (WHO). As there are now no established guidelines for alleviating these symptoms, the efficacy of these treatments is highly questionable. Some high-profile cases in recent years have cast doubt on the long-held belief that this illness is rare and always resolves itself without treatment. We aimed to conduct this review to get a deeper comprehension of the evolving epidemiology of monkeypox by analysing such factors as the number of confirmed, probable, and potential cases, the median age at presentation, the mortality rate, and the geographic distribution of the disease. This study offers an updated review of monkeypox and the clinical treatments that are currently available as a result of the worldwide epidemics.
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Affiliation(s)
- Nishant Johri
- Department of Pharmacy Practice, Teerthanker Mahaveer Hospital & Research Centre, Moradabad, Uttar Pradesh, India,Department of Pharmacy Practice, Teerthanker Mahaveer College of Pharmacy, Moradabad, Uttar Pradesh, India,Corresponding author
| | - Deepanshu Kumar
- Department of Pharmacy Practice, Teerthanker Mahaveer Hospital & Research Centre, Moradabad, Uttar Pradesh, India,Department of Pharmacy Practice, Teerthanker Mahaveer College of Pharmacy, Moradabad, Uttar Pradesh, India
| | - Priya Nagar
- Department of Pharmacy Practice, Teerthanker Mahaveer Hospital & Research Centre, Moradabad, Uttar Pradesh, India,Department of Pharmacy Practice, Teerthanker Mahaveer College of Pharmacy, Moradabad, Uttar Pradesh, India
| | - Aditya Maurya
- Department of Pharmacy Practice, Teerthanker Mahaveer Hospital & Research Centre, Moradabad, Uttar Pradesh, India,Department of Pharmacy Practice, Teerthanker Mahaveer College of Pharmacy, Moradabad, Uttar Pradesh, India
| | - Maheshwari Vengat
- Department of Oncology, Chester Medical School, Chester, United Kingdom
| | - Parag Jain
- Department of Pharmacology, Chhatrapati Shivaji Institute of Pharmacy, Durg, Chhattisgarh 491001, India
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Whole-Genome Sequences of Human Monkeypox Virus Strains from Two 2022 Global Outbreak Cases in Western New York State. Microbiol Resour Announc 2022; 11:e0084622. [DOI: 10.1128/mra.00846-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The genomes of two human monkeypox virus strains from recently reported cases in our local region that were associated with the 2022 global outbreak were sequenced. Genomes from clinical isolates provide valuable information for epidemiological tracking and analysis of strain evolution and can be especially important during the early phases of outbreaks.
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