1
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Li Y, Wang L, Chen S. An overview of the progress made in research into the Mpox virus. Med Res Rev 2024. [PMID: 39318037 DOI: 10.1002/med.22085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 08/05/2024] [Accepted: 09/01/2024] [Indexed: 09/26/2024]
Abstract
Mpox is a zoonotic illness caused by the Mpox virus (MPXV), a member of the Orthopoxvirus family. Although a few cases have been reported outside Africa, it was originally regarded as an endemic disease limited to African countries. However, the Mpox outbreak of 2022 was remarkable in that the infection spread to more than 123 countries worldwide, causing thousands of infections and deaths. The ongoing Mpox outbreak has been declared as a public health emergency of international concern by the World Health Organization. For a better management and control of the epidemic, this review summarizes the research advances and important scientific findings on MPXV by reviewing the current literature on epidemiology, clinical characteristics, diagnostic methods, prevention and treatment measures, and animal models of MPXV. This review provides useful information to raise awareness about the transmission, symptoms, and protective measures of MPXV, serving as a theoretical guide for relevant institutions to control MPXV.
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Affiliation(s)
- Yansheng Li
- Shenzhen Key Laboratory of Microbiology in Genomic Modification & Editing and Application, Medical Innovation Technology Transformation Center of Shenzhen Second People's Hospital, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound lmaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Department of Critical Care Medicine, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Lianrong Wang
- Department of Respiratory Diseases, Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Shi Chen
- Shenzhen Key Laboratory of Microbiology in Genomic Modification & Editing and Application, Medical Innovation Technology Transformation Center of Shenzhen Second People's Hospital, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound lmaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Department of Critical Care Medicine, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
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2
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Scarpa F, Azzena I, Ciccozzi A, Branda F, Locci C, Perra M, Pascale N, Romano C, Ceccarelli G, Terrazzano G, Fiori PL, Ciccozzi M, Casu M, Sanna D. Update of the Genetic Variability of Monkeypox Virus Clade IIb Lineage B.1. Microorganisms 2024; 12:1874. [PMID: 39338547 PMCID: PMC11434445 DOI: 10.3390/microorganisms12091874] [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: 08/09/2024] [Revised: 09/06/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
From 1 January 2022 to 31 May 2024, the World Health Organization (WHO) reported 97,745 laboratory-confirmed Mpox cases, including 203 deaths, across 116 countries. Despite a 2.3% decrease in new cases in May 2024 compared to April 2024, significant regional variations persist. The African Region reported the highest proportion of new cases, while other regions experienced mixed trends. Phylogenomic analyses of the Mpox virus Clade IIb lineage B.1 reveal stable genetic variability with minimal diversification. The Bayesian Skyline Plot indicates a generally stable viral population size with a modest peak in late 2023, followed by a decline. In general, the data indicate that the MPXV outbreak is primarily localized within a few consistent geographic clusters. The virus's evolution is relatively slow, as indicated by its stable genetic variability, and Clade IIb lineage B.1 does not currently show signs of rapid genetic changes or population growth. The current low level of genetic diversity should not lead to complacency. Ongoing genomic surveillance is essential for effective outbreak management and understanding. This monitoring is crucial for identifying any shifts in the virus's behavior or transmission, allowing for prompt public health responses and adjustments. In addition, continued vigilance is necessary to detect any new variants that might influence the outbreak's trajectory.
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Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Ilenia Azzena
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Alessandra Ciccozzi
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Francesco Branda
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, 00128 Roma, Italy
| | - Chiara Locci
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Maria Perra
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Noemi Pascale
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
- Department of Chemical Physical Mathematical and Natural Sciences, University of Sassari, 07100 Sassari, Italy
| | - Chiara Romano
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, 00128 Roma, Italy
| | - Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases, University Hospital Policlinico Umberto I, Sapienza University of Rome, 00161 Rome, Italy
| | | | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Azienza Ospedaliera Universitaria (AOU) Sassari, 07100 Sassari, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, 00128 Roma, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
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3
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Ortigas-Vasquez A, Szpara M. Embracing Complexity: What Novel Sequencing Methods Are Teaching Us About Herpesvirus Genomic Diversity. Annu Rev Virol 2024; 11:67-87. [PMID: 38848592 DOI: 10.1146/annurev-virology-100422-010336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024]
Abstract
The arrival of novel sequencing technologies throughout the past two decades has led to a paradigm shift in our understanding of herpesvirus genomic diversity. Previously, herpesviruses were seen as a family of DNA viruses with low genomic diversity. However, a growing body of evidence now suggests that herpesviruses exist as dynamic populations that possess standing variation and evolve at much faster rates than previously assumed. In this review, we explore how strategies such as deep sequencing, long-read sequencing, and haplotype reconstruction are allowing scientists to dissect the genomic composition of herpesvirus populations. We also discuss the challenges that need to be addressed before a detailed picture of herpesvirus diversity can emerge.
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Affiliation(s)
- Alejandro Ortigas-Vasquez
- Departments of Biology and of Biochemistry and Molecular Biology; Center for Infectious Disease Dynamics; and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA;
| | - Moriah Szpara
- Departments of Biology and of Biochemistry and Molecular Biology; Center for Infectious Disease Dynamics; and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA;
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4
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Carey ME, Thi Nguyen TN, Tran DHN, Dyson ZA, Keane JA, Pham Thanh D, Mylona E, Nair S, Chattaway M, Baker S. The origins of haplotype 58 (H58) Salmonella enterica serovar Typhi. Commun Biol 2024; 7:775. [PMID: 38942806 PMCID: PMC11213900 DOI: 10.1038/s42003-024-06451-8] [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: 12/22/2023] [Accepted: 06/13/2024] [Indexed: 06/30/2024] Open
Abstract
Antimicrobial resistance (AMR) poses a serious threat to the clinical management of typhoid fever. AMR in Salmonella Typhi (S. Typhi) is commonly associated with the H58 lineage, a lineage that arose comparatively recently before becoming globally disseminated. To better understand when and how H58 emerged and became dominant, we performed detailed phylogenetic analyses on contemporary genome sequences from S. Typhi isolated in the period spanning the emergence. Our dataset, which contains the earliest described H58 S. Typhi organism, indicates that ancestral H58 organisms were already multi-drug resistant (MDR). These organisms emerged spontaneously in India in 1987 and became radially distributed throughout South Asia and then globally in the ensuing years. These early organisms were associated with a single long branch, possessing mutations associated with increased bile tolerance, suggesting that the first H58 organism was generated during chronic carriage. The subsequent use of fluoroquinolones led to several independent mutations in gyrA. The ability of H58 to acquire and maintain AMR genes continues to pose a threat, as extensively drug-resistant (XDR; MDR plus resistance to ciprofloxacin and third generation cephalosporins) variants, have emerged recently in this lineage. Understanding where and how H58 S. Typhi originated and became successful is key to understand how AMR drives successful lineages of bacterial pathogens. Additionally, these data can inform optimal targeting of typhoid conjugate vaccines (TCVs) for reducing the potential for emergence and the impact of new drug-resistant variants. Emphasis should also be placed upon the prospective identification and treatment of chronic carriers to prevent the emergence of new drug resistant variants with the ability to spread efficiently.
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Affiliation(s)
- Megan E Carey
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK.
- IAVI, Chelsea & Westminster Hospital, London, UK.
| | - To Nguyen Thi Nguyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Program, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | | | - Zoe A Dyson
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jacqueline A Keane
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Duy Pham Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Program, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Elli Mylona
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Satheesh Nair
- United Kingdom Health Security Agency, Gastrointestinal Bacteria Reference Unit, London, UK
| | - Marie Chattaway
- United Kingdom Health Security Agency, Gastrointestinal Bacteria Reference Unit, London, UK
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
- IAVI, Chelsea & Westminster Hospital, London, UK
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5
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Parker E, Omah IF, Varilly P, Magee A, Ayinla AO, Sijuwola AE, Ahmed MI, Ope-ewe OO, Ogunsanya OA, Olono A, Eromon P, Tomkins-Tinch CH, Otieno JR, Akanbi O, Egwuenu A, Ehiakhamen O, Chukwu C, Suleiman K, Akinpelu A, Ahmad A, Imam KI, Ojedele R, Oripenaye V, Ikeata K, Adelakun S, Olajumoke B, Djuicy DD, Essengue LLM, Yifomnjou MHM, Zeller M, Gangavarapu K, O’Toole Á, Park DJ, Mboowa G, Tessema SK, Tebeje YK, Folarin O, Happi A, Lemey P, Suchard MA, Andersen KG, Sabeti P, Rambaut A, Njoum R, Ihekweazu C, Jide I, Adetifa I, Happi CT. Genomic epidemiology uncovers the timing and origin of the emergence of mpox in humans. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.18.24309104. [PMID: 38947052 PMCID: PMC11213064 DOI: 10.1101/2024.06.18.24309104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Five years before the 2022-2023 global mpox outbreak Nigeria reported its first cases in nearly 40 years, with the ongoing epidemic since driven by sustained human-to-human transmission. However, limited genomic data has left questions about the timing and origin of the mpox virus' (MPXV) emergence. Here we generated 112 MPXV genomes from Nigeria from 2021-2023. We identify the closest zoonotic outgroup to the human epidemic in southern Nigeria, and estimate that the lineage transmitting from human-to-human emerged around July 2014, circulating cryptically until detected in September 2017. The epidemic originated in Southern Nigeria, particularly Rivers State, which also acted as a persistent and dominant source of viral dissemination to other states. We show that APOBEC3 activity increased MPXV's evolutionary rate twenty-fold during human-to-human transmission. We also show how Delphy, a tool for near-real-time Bayesian phylogenetics, can aid rapid outbreak analytics. Our study sheds light on MPXV's establishment in West Africa before the 2022-2023 global outbreak and highlights the need for improved pathogen surveillance and response.
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Affiliation(s)
- Edyth Parker
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ifeanyi F. Omah
- Institute of Ecology and Evolution, University of Edinburgh, The King’s Buildings, Edinburgh EH9 3FL, UK
- Department of Parasitology and Entomology, Nnamdi Azikiwe University, Awka, Nigeria
| | - Patrick Varilly
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andrew Magee
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Akeemat Opeyemi Ayinla
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Ayotunde E. Sijuwola
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Muhammad I. Ahmed
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Oludayo O. Ope-ewe
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Olusola Akinola Ogunsanya
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Alhaji Olono
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Philomena Eromon
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | - Olusola Akanbi
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Abiodun Egwuenu
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | | | - Chimaobi Chukwu
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Kabiru Suleiman
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Afolabi Akinpelu
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Adama Ahmad
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | | | - Richard Ojedele
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Victor Oripenaye
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Kenneth Ikeata
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | | | | | - Delia Doreen Djuicy
- Virology Service, Centre Pasteur du Cameroun, 451 Rue 2005, Yaounde 2, P.O. Box 1274
| | | | | | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Áine O’Toole
- Institute of Ecology and Evolution, University of Edinburgh, The King’s Buildings, Edinburgh EH9 3FL, UK
| | - Daniel J Park
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gerald Mboowa
- Africa Centres for Disease Control and Prevention, P.O. Box 3243, Addis Ababa, Ethiopia
| | | | - Yenew Kebede Tebeje
- Africa Centres for Disease Control and Prevention, P.O. Box 3243, Addis Ababa, Ethiopia
| | - Onikepe Folarin
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Anise Happi
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Marc A Suchard
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Pardis Sabeti
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Immunology and Infectious Diseases, Harvard T H Chan School of Public Health, Boston, MA 02115
| | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, The King’s Buildings, Edinburgh EH9 3FL, UK
| | - Richard Njoum
- Virology Service, Centre Pasteur du Cameroun, 451 Rue 2005, Yaounde 2, P.O. Box 1274
| | - Chikwe Ihekweazu
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Idriss Jide
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Ifedayo Adetifa
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Christian T Happi
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
- Department of Immunology and Infectious Diseases, Harvard T H Chan School of Public Health, Boston, MA 02115
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6
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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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7
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Shan KJ, Wu C, Tang X, Lu R, Hu Y, Tan W, Lu J. Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzad003. [PMID: 38862422 PMCID: PMC11425058 DOI: 10.1093/gpbjnl/qzad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 06/13/2024]
Abstract
The monkeypox virus (mpox virus, MPXV) epidemic in 2022 has posed a significant public health risk. Yet, the evolutionary principles of MPXV remain largely unknown. Here, we examined the evolutionary patterns of protein sequences and codon usage in MPXV. We first demonstrated the signal of positive selection in OPG027, specifically in the Clade I lineage of MPXV. Subsequently, we discovered accelerated protein sequence evolution over time in the variants responsible for the 2022 outbreak. Furthermore, we showed strong epistasis between amino acid substitutions located in different genes. The codon adaptation index (CAI) analysis revealed that MPXV genes tended to use more non-preferred codons compared to human genes, and the CAI decreased over time and diverged between clades, with Clade I > IIa and IIb-A > IIb-B. While the decrease in fatality rate among the three groups aligned with the CAI pattern, it remains unclear whether this correlation was coincidental or if the deoptimization of codon usage in MPXV led to a reduction in fatality rates. This study sheds new light on the mechanisms that govern the evolution of MPXV in human populations.
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Affiliation(s)
- Ke-Jia Shan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
- Sinovac Biotech Ltd., Beijing 100085, China
| | - Changcheng Wu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Roujian Lu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Yaling Hu
- Sinovac Biotech Ltd., Beijing 100085, China
| | - Wenjie Tan
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
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Deiana M, Lavezzari D, Mori A, Accordini S, Pomari E, Piubelli C, Malagò S, Cordioli M, Ronzoni N, Angheben A, Tacconelli E, Capobianchi MR, Gobbi FG, Castilletti C. Exploring Viral Genome Profile in Mpox Patients during the 2022 Outbreak, in a North-Eastern Centre of Italy. Viruses 2024; 16:726. [PMID: 38793608 PMCID: PMC11125733 DOI: 10.3390/v16050726] [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: 04/11/2024] [Revised: 04/28/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
In 2022, an unprecedented outbreak of mpox raged in several nations. Sequences from the 2022 outbreak reveal a higher nucleotide substitution if compared with the estimated rate for orthopoxviruses. Recently, intra-lesion SNVs (single nucleotide variants) have been described, and these have been suggested as possible sources of genetic variation. Until now, it has not been clear if the presence of several SNVs could represents the result of local mutagenesis or a possible co-infection. We investigated the significance of SNVs through whole-genome sequencing analysis of four unrelated mpox cases. In addition to the known mutations harboured by the circulating strains of virus (MPXV), 7 novel mutations were identified, including SNVs located in genes that are involved in immune evasion mechanisms and/or viral fitness, six of these appeared to be APOBEC3-driven. Interestingly, three patients exhibited the coexistence of mutated and wild-type alleles for five non-synonymous variants. In addition, two patients, apparently unrelated, showed an analogous pattern for two novel mutations, albeit with divergent frequencies. The coexistence of mixed viral populations, harbouring non-synonymous mutations in patients, supports the hypothesis of possible co-infection. Additional investigations of larger clinical cohorts are essential to validating intra-patient viral genome heterogeneity and determining the possibility of co-presence events of slightly divergent MPXV strains.
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Affiliation(s)
- Michela Deiana
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy (M.R.C.); (F.G.G.); (C.C.)
| | - Denise Lavezzari
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy (M.R.C.); (F.G.G.); (C.C.)
| | - Antonio Mori
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy (M.R.C.); (F.G.G.); (C.C.)
| | - Silvia Accordini
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy (M.R.C.); (F.G.G.); (C.C.)
| | - Elena Pomari
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy (M.R.C.); (F.G.G.); (C.C.)
| | - Chiara Piubelli
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy (M.R.C.); (F.G.G.); (C.C.)
| | - Simone Malagò
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy (M.R.C.); (F.G.G.); (C.C.)
- PhD National Programme in One Health approaches to infectious diseases and life science research, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy
| | - Maddalena Cordioli
- Division of Infectious Diseases, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy
- Division of Infectious Diseases, Department of Medicine, Verona University Hospital, 37134 Verona, Italy;
| | - Niccolò Ronzoni
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy (M.R.C.); (F.G.G.); (C.C.)
| | - Andrea Angheben
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy (M.R.C.); (F.G.G.); (C.C.)
| | - Evelina Tacconelli
- Division of Infectious Diseases, Department of Medicine, Verona University Hospital, 37134 Verona, Italy;
| | - Maria Rosaria Capobianchi
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy (M.R.C.); (F.G.G.); (C.C.)
| | - Federico Giovanni Gobbi
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy (M.R.C.); (F.G.G.); (C.C.)
- Department of Clinical and Experimental Sciences, University of Brescia, 25121 Brescia, Italy
| | - Concetta Castilletti
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy (M.R.C.); (F.G.G.); (C.C.)
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9
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Hewel C, Schmidt H, Runkel S, Kohnen W, Schweiger-Seemann S, Michel A, Bikar SE, Lieb B, Plachter B, Hankeln T, Linke M, Gerber S. Nanopore adaptive sampling of a metagenomic sample derived from a human monkeypox case. J Med Virol 2024; 96:e29610. [PMID: 38654702 DOI: 10.1002/jmv.29610] [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: 11/06/2023] [Revised: 03/18/2024] [Accepted: 04/05/2024] [Indexed: 04/26/2024]
Abstract
In 2022, a series of human monkeypox cases in multiple countries led to the largest and most widespread outbreak outside the known endemic areas. Setup of proper genomic surveillance is of utmost importance to control such outbreaks. To this end, we performed Nanopore (PromethION P24) and Illumina (NextSeq. 2000) Whole Genome Sequencing (WGS) of a monkeypox sample. Adaptive sampling was applied for in silico depletion of the human host genome, allowing for the enrichment of low abundance viral DNA without a priori knowledge of sample composition. Nanopore sequencing allowed for high viral genome coverage, tracking of sample composition during sequencing, strain determination, and preliminary assessment of mutational pattern. In addition to that, only Nanopore data allowed us to resolve the entire monkeypox virus genome, with respect to two structural variants belonging to the genes OPG015 and OPG208. These SVs in important host range genes seem stable throughout the outbreak and are frequently misassembled and/or misannotated due to the prevalence of short read sequencing or short read first assembly. Ideally, standalone standard Illumina sequencing should not be used for Monkeypox WGS and de novo assembly, since it will obfuscate the structure of the genome, which has an impact on the quality and completeness of the genomes deposited in public databases and thus possibly on the ability to evaluate the complete genetic reason for the host range change of monkeypox in the current pandemic.
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Affiliation(s)
- Charlotte Hewel
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Hanno Schmidt
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Institute for Virology and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Stefan Runkel
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Transfusion Unit & Test Center, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Wolfgang Kohnen
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Department of Hygiene and Infection Prevention, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Susann Schweiger-Seemann
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - André Michel
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Medical Management Department, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Sven-Ernö Bikar
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- StarSEQ GmbH, Mainz, Germany
| | | | - Bodo Plachter
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Institute for Virology and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Thomas Hankeln
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Faculty of Biology, Institute of Organismic and Molecular Evolution, Molecular Genetics & Genome Analysis, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Matthias Linke
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
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10
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Diaz-Cánova D, Moens U, Brinkmann A, Nitsche A, Okeke MI. Whole genome sequencing of recombinant viruses obtained from co-infection and superinfection of Vero cells with modified vaccinia virus ankara vectored influenza vaccine and a naturally occurring cowpox virus. Front Immunol 2024; 15:1277447. [PMID: 38633245 PMCID: PMC11021749 DOI: 10.3389/fimmu.2024.1277447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
Modified vaccinia virus Ankara (MVA) has been widely tested in clinical trials as recombinant vector vaccine against infectious diseases and cancers in humans and animals. However, one biosafety concern about the use of MVA vectored vaccine is the potential for MVA to recombine with naturally occurring orthopoxviruses in cells and hosts in which it multiplies poorly and, therefore, producing viruses with mosaic genomes with altered genetic and phenotypic properties. We previously conducted co-infection and superinfection experiments with MVA vectored influenza vaccine (MVA-HANP) and a feline Cowpox virus (CPXV-No-F1) in Vero cells (that were semi-permissive to MVA infection) and showed that recombination occurred in both co-infected and superinfected cells. In this study, we selected the putative recombinant viruses and performed genomic characterization of these viruses. Some putative recombinant viruses displayed plaque morphology distinct of that of the parental viruses. Our analysis demonstrated that they had mosaic genomes of different lengths. The recombinant viruses, with a genome more similar to MVA-HANP (>50%), rescued deleted and/or fragmented genes in MVA and gained new host ranges genes. Our analysis also revealed that some MVA-HANP contained a partially deleted transgene expression cassette and one recombinant virus contained part of the transgene expression cassette similar to that incomplete MVA-HANP. The recombination in co-infected and superinfected Vero cells resulted in recombinant viruses with unpredictable biological and genetic properties as well as recovery of delete/fragmented genes in MVA and transfer of the transgene into replication competent CPXV. These results are relevant to hazard characterization and risk assessment of MVA vectored biologicals.
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Affiliation(s)
- Diana Diaz-Cánova
- Molecular Inflammation Research Group, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Ugo Moens
- Molecular Inflammation Research Group, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Annika Brinkmann
- WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Andreas Nitsche
- WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Malachy Ifeanyi Okeke
- Section of Biomedical Sciences, Department of Natural and Environmental Sciences, School of Arts and Sciences, American University of Nigeria, Yola, Nigeria
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11
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Paredes MI, Ahmed N, Figgins M, Colizza V, Lemey P, McCrone JT, Müller N, Tran-Kiem C, Bedford T. Underdetected dispersal and extensive local transmission drove the 2022 mpox epidemic. Cell 2024; 187:1374-1386.e13. [PMID: 38428425 PMCID: PMC10962340 DOI: 10.1016/j.cell.2024.02.003] [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: 10/04/2023] [Revised: 12/15/2023] [Accepted: 02/02/2024] [Indexed: 03/03/2024]
Abstract
The World Health Organization declared mpox a public health emergency of international concern in July 2022. To investigate global mpox transmission and population-level changes associated with controlling spread, we built phylogeographic and phylodynamic models to analyze MPXV genomes from five global regions together with air traffic and epidemiological data. Our models reveal community transmission prior to detection, changes in case reporting throughout the epidemic, and a large degree of transmission heterogeneity. We find that viral introductions played a limited role in prolonging spread after initial dissemination, suggesting that travel bans would have had only a minor impact. We find that mpox transmission in North America began declining before more than 10% of high-risk individuals in the USA had vaccine-induced immunity. Our findings highlight the importance of broader routine specimen screening surveillance for emerging infectious diseases and of joint integration of genomic and epidemiological information for early outbreak control.
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Affiliation(s)
- Miguel I Paredes
- Department of Epidemiology, University of Washington, Seattle, WA, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Nashwa Ahmed
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Marlin Figgins
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, Paris, France
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - John T McCrone
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Nicola Müller
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Cécile Tran-Kiem
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Trevor Bedford
- Department of Epidemiology, University of Washington, Seattle, WA, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA
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12
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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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13
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Zhang S, Li YD, Cai YR, Kang XP, Feng Y, Li YC, Chen YH, Li J, Bao LL, Jiang T. Compositional features analysis by machine learning in genome represents linear adaptation of monkeypox virus. Front Genet 2024; 15:1361952. [PMID: 38495668 PMCID: PMC10940399 DOI: 10.3389/fgene.2024.1361952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/21/2024] [Indexed: 03/19/2024] Open
Abstract
Introduction: The global headlines have been dominated by the sudden and widespread outbreak of monkeypox, a rare and endemic zoonotic disease caused by the monkeypox virus (MPXV). Genomic composition based machine learning (ML) methods have recently shown promise in identifying host adaptability and evolutionary patterns of virus. Our study aimed to analyze the genomic characteristics and evolutionary patterns of MPXV using ML methods. Methods: The open reading frame (ORF) regions of full-length MPXV genomes were filtered and 165 ORFs were selected as clusters with the highest homology. Unsupervised machine learning methods of t-distributed stochastic neighbor embedding (t-SNE), Principal Component Analysis (PCA), and hierarchical clustering were performed to observe the DCR characteristics of the selected ORF clusters. Results: The results showed that MPXV sequences post-2022 showed an obvious linear adaptive evolution, indicating that it has become more adapted to the human host after accumulating mutations. For further accurate analysis, the ORF regions with larger variations were filtered out based on the ranking of homology difference to narrow down the key ORF clusters, which drew the same conclusion of linear adaptability. Then key differential protein structures were predicted by AlphaFold 2, which meant that difference in main domains might be one of the internal reasons for linear adaptive evolution. Discussion: Understanding the process of linear adaptation is critical in the constant evolutionary struggle between viruses and their hosts, playing a significant role in crafting effective measures to tackle viral diseases. Therefore, the present study provides valuable insights into the evolutionary patterns of the MPXV in 2022 from the perspective of genomic composition characteristics analysis through ML methods.
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Affiliation(s)
- Sen Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Ya-Dan Li
- College of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Yu-Rong Cai
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
- College of the First Clinical Medical, Inner Mongolia Medical University, Hohhot, China
| | - Xiao-Ping Kang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Ye Feng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yu-Chang Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yue-Hong Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Jing Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
- College of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Li-Li Bao
- College of Basic Medical Sciences, Inner Mongolia Medical University, Hohhot, China
| | - Tao Jiang
- College of Basic Medical Sciences, Anhui Medical University, Hefei, China
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14
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Davidson I, Lupini C, Catelli E, Quaglia G, Maddaloni L, Mescolini G. Virulence evaluation of Israeli Marek's disease virus isolates from commercial poultry using their meq gene sequence. Virus Genes 2024; 60:32-43. [PMID: 38184501 DOI: 10.1007/s11262-023-02042-7] [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: 09/26/2023] [Accepted: 11/17/2023] [Indexed: 01/08/2024]
Abstract
Fifty-seven Gallid alphaherpesvirus 2 (GaHV-2) isolates, collected during a 30-year period (1990-2019) from commercial poultry flocks affected by Marek's disease (MD), were molecularly characterised. The GaHV-2 meq gene was amplified and sequenced to evaluate the virus virulence, based on the number of PPPPs within the proline-rich repeats (PRRs) of its transactivation domain. The present illustration of virus virulence evaluation on a large scale of field virus isolates by molecular analysis exemplifies the practical benefit and usefulness of the molecular marker in commercial GaVH-2 isolates. The alternative assay of GaVH-2 virulence pathotyping is the classical Gold Standard ADOL method, which is difficult and impossible to employ on a large scale using the Specific Pathogen Free (SPF) chicks of the ADOL strains kept in isolators for two months. The phylogenetic analysis performed in the present study showed that the meq gene amino acid sequences of the 57 Israeli strains divide into 16 phylogenetic branches. The virulence evaluation was performed in comparison with 36 GaHV-2 prototype strains, previously characterised by the in vivo Gold Standard ADOL assay. The results obtained revealed that the GaHV-2 strains circulating in Israel have evolved into a higher virulence potential during the years, as the four-proline stretches number in the meq gene decreased over the investigated period, typically of very virulent virus prototypes. The present study supports the meq gene molecular markers for the assessment of field GaVH-2 strains virulence.
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Affiliation(s)
| | - Caterina Lupini
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Bologna, Italy
| | - Elena Catelli
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Bologna, Italy
| | - Giulia Quaglia
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Bologna, Italy
| | - Luca Maddaloni
- Department of Public Health and Infectious Diseases, Sapienza, University of Rome, Rome, Italy
| | - Giulia Mescolini
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Bologna, Italy
- Operating Unit of Animal Health and Hygiene of Livestock Production, Department of Public Health, AUSL della Romagna, Forlì, FC, Italy
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15
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Allen A, Magee R, Devaney R, Ardis T, McNally C, McCormick C, Presho E, Doyle M, Ranasinghe P, Johnston P, Kirke R, Harwood R, Farrell D, Kenny K, Smith J, Gordon S, Ford T, Thompson S, Wright L, Jones K, Prodohl P, Skuce R. Whole-Genome sequencing in routine Mycobacterium bovis epidemiology - scoping the potential. Microb Genom 2024; 10:001185. [PMID: 38354031 PMCID: PMC10926703 DOI: 10.1099/mgen.0.001185] [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: 10/23/2023] [Accepted: 01/09/2024] [Indexed: 02/16/2024] Open
Abstract
Mycobacterium bovis the main agent of bovine tuberculosis (bTB), presents as a series of spatially-localised micro-epidemics across landscapes. Classical molecular typing methods applied to these micro-epidemics, based on genotyping a few variable loci, have significantly improved our understanding of potential epidemiological links between outbreaks. However, they have limited utility owing to low resolution. Conversely, whole-genome sequencing (WGS) provides the highest resolution data available for molecular epidemiology, producing richer outbreak tracing, insights into phylogeography and epidemic evolutionary history. We illustrate these advantages by focusing on a common single lineage of M. bovis (1.140) from Northern Ireland. Specifically, we investigate the spatial sub-structure of 20 years of herd-level multi locus VNTR analysis (MLVA) surveillance data and WGS data from a down sampled subset of isolates of this MLVA type over the same time frame. We mapped 2108 isolate locations of MLVA type 1.140 over the years 2000-2022. We also mapped the locations of 148 contemporary WGS isolates from this lineage, over a similar geographic range, stratifying by single nucleotide polymorphism (SNP) relatedness cut-offs of 15 SNPs. We determined a putative core range for the 1.140 MLVA type and SNP-defined sequence clusters using a 50 % kernel density estimate, using cattle movement data to inform on likely sources of WGS isolates found outside of core ranges. Finally, we applied Bayesian phylogenetic methods to investigate past population history and reproductive number of the 1.140 M. bovis lineage. We demonstrate that WGS SNP-defined clusters exhibit smaller core ranges than the established MLVA type - facilitating superior disease tracing. We also demonstrate the superior functionality of WGS data in determining how this lineage was disseminated across the landscape, likely via cattle movement and to infer how its effective population size and reproductive number has been in flux since its emergence. These initial findings highlight the potential of WGS data for routine monitoring of bTB outbreaks.
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Affiliation(s)
- Adrian Allen
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Ryan Magee
- Queen’s University Belfast, school of Biological Sciences, UK
| | - Ryan Devaney
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Tara Ardis
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Caitlín McNally
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Carl McCormick
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Eleanor Presho
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Michael Doyle
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Purnika Ranasinghe
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Philip Johnston
- Department of Agriculture, Environment and Rural Affairs for Northern Ireland, Belfast, UK
| | - Raymond Kirke
- Department of Agriculture, Environment and Rural Affairs for Northern Ireland, Belfast, UK
| | - Roland Harwood
- Department of Agriculture, Environment and Rural Affairs for Northern Ireland, Belfast, UK
| | - Damien Farrell
- Central Veterinary Research Laboratory, Kildare, Ireland
- University College Dublin, Dublin, Ireland
| | - Kevin Kenny
- Central Veterinary Research Laboratory, Kildare, Ireland
| | | | | | - Tom Ford
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Suzan Thompson
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Lorraine Wright
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Kerri Jones
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Paulo Prodohl
- Queen’s University Belfast, school of Biological Sciences, UK
| | - Robin Skuce
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
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16
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Ortigas-Vasquez A, Pandey U, Renner D, Bowen C, Baigent SJ, Dunn J, Cheng H, Yao Y, Read AF, Nair V, Kennedy DA, Szpara ML. Comparative Analysis of Multiple Consensus Genomes of the Same Strain of Marek's Disease Virus Reveals Intrastrain Variation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.04.556264. [PMID: 37732198 PMCID: PMC10508761 DOI: 10.1101/2023.09.04.556264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Current strategies to understand the molecular basis of Marek's disease virus (MDV) virulence primarily consist of cataloguing divergent nucleotides between strains with different phenotypes. However, each MDV strain is typically represented by a single consensus genome despite the confirmed existence of mixed viral populations. To assess the reliability of single-consensus interstrain genomic comparisons, we obtained two additional consensus genomes of vaccine strain CVI988 (Rispens) and two additional consensus genomes of the very virulent strain Md5 by sequencing viral stocks and cultured field isolates. In conjunction with the published genomes of CVI988 and Md5, this allowed us to perform 3-way comparisons between consensus genomes of the same strain. We found that consensus genomes of CVI988 can vary in as many as 236 positions involving 13 open reading frames (ORFs). In contrast, we found that Md5 genomes varied only in 11 positions involving a single ORF. Phylogenomic analyses showed all three Md5 consensus genomes clustered closely together, while also showing that CVI988 GenBank.BAC diverged from CVI988 Pirbright.lab and CVI988 USDA.PA.field . Comparison of CVI988 consensus genomes revealed 19 SNPs in the unique regions of CVI988 GenBank.BAC that were not present in either CVI988 Pirbright.lab or CVI988 USDA.PA.field . Finally, we evaluated the genomic heterogeneity of CVI988 and Md5 populations by identifying positions with >2% read support for alternative alleles in two ultra-deeply sequenced samples. We were able to confirm that both populations of CVI988 and Md5 were mixed, exhibiting a total of 29 and 27 high-confidence minor variant positions, respectively. We did not find any evidence of minor variants in the positions corresponding to the 19 SNPs in the unique regions of CVI988 GenBank.BAC . Taken together, our findings confirm that consensus genomes of the same strain of MDV can vary and suggest that multiple consensus genomes per strain are needed in order to maximize the accuracy of interstrain genomic comparisons.
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17
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Kalaba MH, El-Sherbiny GM, Sharaf MH, Farghal EE. Biological Characteristics and Pathogenesis of Monkeypox Virus: An Overview. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1451:91-109. [PMID: 38801573 DOI: 10.1007/978-3-031-57165-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Although the smallpox virus has been eradicated worldwide, the World Health Organization (WHO) has issued a warning about the virus's potential to propagate globally. The WHO labeled monkeypox a world public health emergency in July 2022, requiring urgent prevention and treatment. The monkeypox virus is a part of the Poxviridae family, Orthopoxvirus genus, and is accountable for smallpox, which has killed over a million people in the past. Natural hosts of the virus include squirrels, Gambian rodents, chimpanzees, and other monkeys. The monkeypox virus has transmitted to humans through primary vectors (various animal species) and secondary vectors, including direct touch with lesions, breathing particles from body fluids, and infected bedding. The viral particles are ovoid or brick-shaped, 200-250 nm in diameter, contain a single double-stranded DNA molecule, and reproduce only in the cytoplasm of infected cells. Monkeypox causes fever, cold, muscle pains, headache, fatigue, and backache. The phylogenetic investigation distinguished between two genetic clades of monkeypox: the more pathogenic Congo Basin clade and the West Africa clade. In recent years, the geographical spread of the human monkeypox virus has accelerated despite a paucity of information regarding the disease's emergence, ecology, and epidemiology. Using lesion samples and polymerase chain reaction (PCR), the monkeypox virus was diagnosed. In the USA, the improved Ankara vaccine can now be used to protect people who are at a higher risk of getting monkeypox. Antivirals that we have now work well against smallpox and may stop the spread of monkeypox, but there is no particular therapy for monkeypox.
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Affiliation(s)
- Mohamed H Kalaba
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Cairo, 11884, Egypt
| | - Gamal M El-Sherbiny
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Cairo, 11884, Egypt.
| | - Mohammed H Sharaf
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Cairo, 11884, Egypt
| | - Eman E Farghal
- Clinical and Chemical Pathology, Faculty of Medicine, Tanta University, Tanta, Egypt
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18
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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] [MESH Headings] [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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19
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Fiddaman SR, Dimopoulos EA, Lebrasseur O, du Plessis L, Vrancken B, Charlton S, Haruda AF, Tabbada K, Flammer PG, Dascalu S, Marković N, Li H, Franklin G, Symmons R, Baron H, Daróczi-Szabó L, Shaymuratova DN, Askeyev IV, Putelat O, Sana M, Davoudi H, Fathi H, Mucheshi AS, Vahdati AA, Zhang L, Foster A, Sykes N, Baumberg GC, Bulatović J, Askeyev AO, Askeyev OV, Mashkour M, Pybus OG, Nair V, Larson G, Smith AL, Frantz LAF. Ancient chicken remains reveal the origins of virulence in Marek's disease virus. Science 2023; 382:1276-1281. [PMID: 38096384 DOI: 10.1126/science.adg2238] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 10/25/2023] [Indexed: 12/18/2023]
Abstract
The pronounced growth in livestock populations since the 1950s has altered the epidemiological and evolutionary trajectory of their associated pathogens. For example, Marek's disease virus (MDV), which causes lymphoid tumors in chickens, has experienced a marked increase in virulence over the past century. Today, MDV infections kill >90% of unvaccinated birds, and controlling it costs more than US$1 billion annually. By sequencing MDV genomes derived from archeological chickens, we demonstrate that it has been circulating for at least 1000 years. We functionally tested the Meq oncogene, one of 49 viral genes positively selected in modern strains, demonstrating that ancient MDV was likely incapable of driving tumor formation. Our results demonstrate the power of ancient DNA approaches to trace the molecular basis of virulence in economically relevant pathogens.
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Affiliation(s)
| | - Evangelos A Dimopoulos
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Ophélie Lebrasseur
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS/Université Toulouse III Paul Sabatier, Toulouse, France
- Instituto Nacional de Antropología y Pensamiento Latinoamericano, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Louis du Plessis
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium
| | - Sophy Charlton
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Ashleigh F Haruda
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Kristina Tabbada
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | | | | | | | - Hannah Li
- Institute of Immunity and Transplantation, University College London, London, UK
| | | | | | | | | | - Dilyara N Shaymuratova
- Laboratory of Biomonitoring, The Institute of Problems in Ecology and Mineral Wealth, Tatarstan Academy of Sciences, Kazan, Russia
| | - Igor V Askeyev
- Laboratory of Biomonitoring, The Institute of Problems in Ecology and Mineral Wealth, Tatarstan Academy of Sciences, Kazan, Russia
| | | | - Maria Sana
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Hossein Davoudi
- Bioarchaeology Laboratory, Central Laboratory, University of Tehran, Tehran, Iran
| | - Homa Fathi
- Bioarchaeology Laboratory, Central Laboratory, University of Tehran, Tehran, Iran
| | - Amir Saed Mucheshi
- Department of Art and Architecture, Payame Noor University (PNU), Tehran, Iran
| | - Ali Akbar Vahdati
- Iranian Ministry of Cultural Heritage, Tourism, and Handicrafts, North Khorasan Office, Iran
| | - Liangren Zhang
- Department of Archaeology, School of History, Nanjing University, China
| | | | - Naomi Sykes
- Department of Archaeology, University of Exeter, Exeter, UK
| | - Gabrielle Cass Baumberg
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Jelena Bulatović
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | - Arthur O Askeyev
- Laboratory of Biomonitoring, The Institute of Problems in Ecology and Mineral Wealth, Tatarstan Academy of Sciences, Kazan, Russia
| | - Oleg V Askeyev
- Laboratory of Biomonitoring, The Institute of Problems in Ecology and Mineral Wealth, Tatarstan Academy of Sciences, Kazan, Russia
| | - Marjan Mashkour
- Bioarchaeology Laboratory, Central Laboratory, University of Tehran, Tehran, Iran
- CNRS, National Museum Natural History Paris, Paris, France
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK
| | - Venugopal Nair
- Department of Biology, University of Oxford, Oxford, UK
- Viral Oncogenesis Group, Pirbright Institute, Woking, UK
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | | | - Laurent A F Frantz
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universitat, Munich, Germany
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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20
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Franzo G, Faustini G, Tucciarone CM, Pasotto D, Legnardi M, Cecchinato M. Conflicting Evidence between Clinical Perception and Molecular Epidemiology: The Case of Fowl Adenovirus D. Animals (Basel) 2023; 13:3851. [PMID: 38136888 PMCID: PMC10741239 DOI: 10.3390/ani13243851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Fowl adenoviruses (FAdVs, species FAdV-A/-E) are responsible for several clinical syndromes reported with increasing frequency in poultry farms in the last decades. In the present study, a phylodynamic analysis was performed on a group of FAdV-D Hexon sequences with adequate available metadata. The obtained results demonstrated the long-term circulation of this species, at least several decades before the first identification of the disease. After a period of progressive increase, the viral population showed a high-level circulation from approximately the 1960s to the beginning of the new millennium, mirroring the expansion of intensive poultry production and animal trade. At the same time, strain migration occurred mainly from Europe to other continents, although other among-continent connections were estimated. Thereafter, the viral population declined progressively, likely due to the improved control measures, potentially including the development and application of FAdV vaccines. An increase in the viral evolutionary rate featured this phase. A role of vaccine-induced immunity in shaping viral evolution could thus be hypothesized. Accordingly, several sites of the Hexon, especially those targeted by the host response were proven under a significant pervasive or episodic diversifying selection. The present study results demonstrate the role of intensive poultry production and market globalization in the rise of FAdV. The applied control strategies, on the other hand, were effective in limiting viral circulation and shaping its evolution.
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Affiliation(s)
- Giovanni Franzo
- Department of Animal Medicine, Production and Health, University of Padua, Viale dell’Università, 16, 35020 Legnaro, Italy; (G.F.); (C.M.T.); (D.P.); (M.L.); (M.C.)
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21
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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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22
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Patiño LH, Guerra S, Muñoz M, Luna N, Farrugia K, van de Guchte A, Khalil Z, Gonzalez-Reiche AS, Hernandez MM, Banu R, Shrestha P, Liggayu B, Firpo Betancourt A, Reich D, Cordon-Cardo C, Albrecht R, Pearl R, Simon V, Rooker A, Sordillo EM, van Bakel H, García-Sastre A, Bogunovic D, Palacios G, Paniz Mondolfi A, Ramírez JD. Phylogenetic landscape of Monkeypox Virus (MPV) during the early outbreak in New York City, 2022. Emerg Microbes Infect 2023; 12:e2192830. [PMID: 36927408 PMCID: PMC10114986 DOI: 10.1080/22221751.2023.2192830] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/14/2023] [Indexed: 03/18/2023]
Abstract
Monkeypox (MPOX) is a zoonotic disease endemic to regions of Central/Western Africa. The geographic endemicity of MPV has expanded, broadening the human-monkeypox virus interface and its potential for spillover. Since May 2022, a large multi-country MPV outbreak with no proven links to endemic countries has originated in Europe and has rapidly expanded around the globe, setting off genomic surveillance efforts. Here, we conducted a genomic analysis of 23 MPV-infected patients from New York City during the early outbreak, assessing the phylogenetic relationship of these strains against publicly available MPV genomes. Additionally, we compared the genomic sequences of clinical isolates versus culture-passaged samples from a subset of samples. Phylogenetic analysis revealed that MPV genomes included in this study cluster within the B.1 lineage (Clade IIb), with some of the samples displaying further differentiation into five different sub-lineages of B.1. Mutational analysis revealed 55 non-synonymous polymorphisms throughout the genome, with some of these mutations located in critical regions required for viral multiplication, structural and assembly functions, as well as the target region for antiviral treatment. In addition, we identified a large majority of polymorphisms associated with GA > AA and TC > TT nucleotide replacements, suggesting the action of human APOBEC3 enzyme. A comparison between clinical isolates and cell culture-passaged samples failed to reveal any difference. Our results provide a first glance at the mutational landscape of early MPV-2022 (B.1) circulating strains in NYC.
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Affiliation(s)
- Luz H. Patiño
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Susana Guerra
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marina Muñoz
- Facultad de Ciencias Naturales, Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Universidad del Rosario, Bogotá, Colombia
| | - Nicolas Luna
- Facultad de Ciencias Naturales, Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Universidad del Rosario, Bogotá, Colombia
| | - Keith Farrugia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zain Khalil
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Matthew M. Hernandez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Radhika Banu
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paras Shrestha
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bernadette Liggayu
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo Firpo Betancourt
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David Reich
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Randy Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rebecca Pearl
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Viviana Simon
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aria Rooker
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo García-Sastre
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dusan Bogunovic
- Department of Microbiology, Centre for Inborn Errors of Immunity, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gustavo Palacios
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alberto Paniz Mondolfi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Juan David Ramírez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Facultad de Ciencias Naturales, Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Universidad del Rosario, Bogotá, Colombia
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23
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Suspène R, Raymond KA, Boutin L, Guillier S, Lemoine F, Ferraris O, Tournier JN, Iseni F, Simon-Lorière E, Vartanian JP. APOBEC3F Is a Mutational Driver of the Human Monkeypox Virus Identified in the 2022 Outbreak. J Infect Dis 2023; 228:1421-1429. [PMID: 37224627 PMCID: PMC11009509 DOI: 10.1093/infdis/jiad165] [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: 02/14/2023] [Revised: 04/24/2023] [Accepted: 05/12/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND On May 6, 2022, a powerful outbreak of monkeypox virus (MPXV) had been reported outside of Africa, with many continuing new cases being reported around the world. Analysis of mutations among the 2 different lineages present in the 2021 and 2022 outbreaks revealed the presence of G->A mutations occurring in the 5'GpA context, indicative of APOBEC3 cytidine deaminase activity. METHODS By using a sensitive polymerase chain reaction (differential DNA denaturation PCR) method allowing differential amplification of AT-rich DNA, we analyzed the level of APOBEC3-induced MPXV editing in infected cells and in patients. RESULTS We demonstrate that G->A hypermutated MPXV genomes can be recovered experimentally from APOBEC3 transfection followed by MPXV infection. Here, among the 7 human APOBEC3 cytidine deaminases (A3A-A3C, A3DE, A3F-A3H), only APOBEC3F was capable of extensively deaminating cytidine residues in MPXV genomes. Hyperedited genomes were also recovered in ∼42% of analyzed patients. Moreover, we demonstrate that substantial repair of these mutations occurs. Upon selection, corrected G->A mutations escaping drift loss contribute to the MPXV evolution observed in the current epidemic. CONCLUSIONS Stochastic or transient overexpression of the APOBEC3F gene exposes the MPXV genome to a broad spectrum of mutations that may be modeling the mutational landscape after multiple cycles of viral replication.
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Affiliation(s)
- Rodolphe Suspène
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Kyle A Raymond
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
- Sorbonne Université, Complexité du Vivant, Paris, France
| | - Laetitia Boutin
- Microbiology and Infectious Diseases Department, Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
- Institut de Recherche Biomédicale des Armées, National Reference Center for Orthopoxviruses, (CNR-LE Orthopoxvirus), Brétigny-sur-Orge, France
| | - Sophie Guillier
- Microbiology and Infectious Diseases Department, Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
| | - Frédéric Lemoine
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Olivier Ferraris
- Microbiology and Infectious Diseases Department, Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
- Institut de Recherche Biomédicale des Armées, National Reference Center for Orthopoxviruses, (CNR-LE Orthopoxvirus), Brétigny-sur-Orge, France
| | - Jean-Nicolas Tournier
- Microbiology and Infectious Diseases Department, Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
- Ecole du Val-de-Grâce, Paris, France
| | - Frédéric Iseni
- Microbiology and Infectious Diseases Department, Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
| | - Etienne Simon-Lorière
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, Paris, France
| | - Jean-Pierre Vartanian
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
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24
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Buchholz HH, Bolaños LM, Bell AG, Michelsen ML, Allen MJ, Temperton B. Novel pelagiphage isolate Polarivirus skadi is a polar specialist that dominates SAR11-associated bacteriophage communities at high latitudes. THE ISME JOURNAL 2023; 17:1660-1670. [PMID: 37452097 PMCID: PMC10504331 DOI: 10.1038/s41396-023-01466-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023]
Abstract
The SAR11 clade are the most abundant members of surface marine bacterioplankton and a critical component of global biogeochemical cycles. Similarly, pelagiphages that infect SAR11 are ubiquitous and highly abundant in the oceans. Pelagiphages are predicted to shape SAR11 community structures and increase carbon turnover throughout the oceans. Yet, ecological drivers of host and niche specificity of pelagiphage populations are poorly understood. Here we report the global distribution of a novel pelagiphage called "Polarivirus skadi", which is the sole representative of a novel genus. P. skadi was isolated from the Western English Channel using a cold-water ecotype of SAR11 as bait. P. skadi is closely related to the globally dominant pelagiphage HTVC010P. Along with other HTVC010P-type viruses, P. skadi belongs to a distinct viral family within the order Caudovirales, for which we propose the name Ubiqueviridae. Metagenomic read recruitment identified P. skadi as one of the most abundant pelagiphages on Earth. P. skadi is a polar specialist, replacing HTVC010P at high latitudes. Experimental evaluation of P. skadi host range against cold- and warm-water SAR11 ecotypes supported cold-water specialism. Relative abundance of P. skadi in marine metagenomes correlated negatively with temperature, and positively with nutrients, available oxygen, and chlorophyll concentrations. In contrast, relative abundance of HTVC010P correlated negatively with oxygen and positively with salinity, with no significant correlation to temperature. The majority of other pelagiphages were scarce in most marine provinces, with a few representatives constrained to discrete ecological niches. Our results suggest that pelagiphage populations persist within a global viral seed bank, with environmental parameters and host availability selecting for a few ecotypes that dominate ocean viromes.
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Affiliation(s)
| | | | - Ashley G Bell
- School of Biosciences, University of Exeter, Exeter, UK
| | | | | | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, UK.
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Molina IS, Jimenez-Vasquez V, Lizarraga W, Sevilla N, Hurtado V, Padilla-Rojas C. Sub-lineage B.1.6 of hMPXV in a global context: Phylogeny and epidemiology. J Med Virol 2023; 95:e29056. [PMID: 37671858 DOI: 10.1002/jmv.29056] [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: 04/29/2023] [Revised: 07/26/2023] [Accepted: 08/14/2023] [Indexed: 09/07/2023]
Abstract
During the 2022 COVID-19 pandemic, monkeypox emerged as a significant threat to global health. The virus responsible for the disease, the human monkeypox virus (hMPXV), underwent various genetic changes, resulting in the emergence of over a dozen distinct lineages, which could be identified by only a small number of unique mutations. As of January 25, 2023, genomic information of hMPXV generated had reached 4632 accessions in the GISAID database. In this study, we aimed to investigate the epidemiological and phylogenetic characteristics of the B.1.6 sub-lineage of hMPXV in Peru, compared with other circulating sub-lineages during the global outbreak. The B.1.6 sub-lineage, characterized by the 111029G>A mutation, was estimated to have emerged in June 2022 and was found mainly in Peru. Most cases (95.8%) were men with an average age of 33 years, and nearly half of the patients had HIV, of whom only 77.35% received antiretroviral therapy. Our findings revealed that the B.1.6, B.1.4, and B.1.2 sub-lineages were well represented and had a higher number of mutations despite having the lowest media substitution rates per site per year. Moreover, it was estimated that B.1.2 and B.1.4 appeared in February 2022 and were the first two sub-lineages to emerge. A mutation profile was also obtained for each sub-lineage, reflecting that several mutations had a pattern similar to the characteristic mutation. This study provides the first estimation of the substitution rate and ancestry of each monkeypox sub-lineage belonging to the 2022 outbreak. Based on our findings, continued genomic surveillance of monkeypox is necessary to understand better and track the evolution of the virus.
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Affiliation(s)
- Iris S Molina
- Area de Innovacion y Desarrollo Tecnológico, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Victor Jimenez-Vasquez
- Area de Innovacion y Desarrollo Tecnológico, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Wendy Lizarraga
- Area de Innovacion y Desarrollo Tecnológico, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Nieves Sevilla
- Area de Innovacion y Desarrollo Tecnológico, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Veronica Hurtado
- Area de Innovacion y Desarrollo Tecnológico, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Carlos Padilla-Rojas
- Area de Innovacion y Desarrollo Tecnológico, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
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26
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Billard E, Barro M, Sérémé D, Bangratz M, Wonni I, Koala M, Kassankogno AI, Hébrard E, Thébaud G, Brugidou C, Poulicard N, Tollenaere C. Dynamics of the rice yellow mottle disease in western Burkina Faso: Epidemic monitoring, spatio-temporal variation of viral diversity, and pathogenicity in a disease hotspot. Virus Evol 2023; 9:vead049. [PMID: 37649958 PMCID: PMC10465090 DOI: 10.1093/ve/vead049] [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: 04/03/2023] [Revised: 07/04/2023] [Accepted: 08/20/2023] [Indexed: 09/01/2023] Open
Abstract
The rice yellow mottle virus (RYMV) is a model in plant virus molecular epidemiology, with the reconstruction of historical introduction routes at the scale of the African continent. However, information on patterns of viral prevalence and viral diversity over multiple years at a local scale remains scarce, in spite of potential implications for crop protection. Here, we describe a 5-year (2015-9) monitoring of RYMV prevalence in six sites from western Burkina Faso (geographic areas of Bama, Banzon, and Karfiguela). It confirmed one irrigated site as a disease hotspot and also found one rainfed lowland (RL) site with occasional high prevalence levels. Within the studied fields, a pattern of disease aggregation was evidenced at a 5-m distance, as expected for a mechanically transmitted virus. Next, we monitored RYMV genetic diversity in the irrigated disease hotspot site, revealing a high viral diversity, with the current coexistence of various distinct genetic groups at the site scale (ca. 520 ha) and also within various specific fields (25 m side). One genetic lineage, named S1bzn, is the most recently emerged group and increased in frequency over the studied period (from 20 per cent or less in 2015-6 to more than 65 per cent in 2019). Its genome results from a recombination between two other lineages (S1wa and S1ca). Finally, experimental work revealed that three rice varieties commonly cultivated in Burkina Faso were not different in terms of resistance level, and we also found no significant effect of RYMV genetic groups on symptom expression and viral load. We found, however, that infection outcome depended on the specific RYMV isolate, with two isolates from the lineage S1bzn accumulating at the highest level at early infections. Overall, this study documents a case of high viral prevalence, high viral diversity, and co-occurrence of divergent genetic lineages at a small geographic scale. A recently emerged lineage, which comprises viral isolates inducing severe symptoms and high accumulation under controlled conditions, could be recently rising through natural selection. Following up the monitoring of RYMV diversity is required to confirm this trend and further understand the factors driving the local maintenance of viral diversity.
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Affiliation(s)
- Estelle Billard
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Mariam Barro
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Drissa Sérémé
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Virologie et de Biologie Végétale, Kamboinsé, Burkina Faso
| | - Martine Bangratz
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Issa Wonni
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Moustapha Koala
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Virologie et de Biologie Végétale, Kamboinsé, Burkina Faso
| | - Abalo Itolou Kassankogno
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Eugénie Hébrard
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Gaël Thébaud
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Christophe Brugidou
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Nils Poulicard
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Charlotte Tollenaere
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
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27
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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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28
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Ghosh N, Chacko L, Vallamkondu J, Banerjee T, Sarkar C, Singh B, Kalra RS, Bhatti JS, Kandimalla R, Dewanjee S. Clinical Strategies and Therapeutics for Human Monkeypox Virus: A Revised Perspective on Recent Outbreaks. Viruses 2023; 15:1533. [PMID: 37515218 PMCID: PMC10384767 DOI: 10.3390/v15071533] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/03/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
An enveloped double-stranded DNA monkeypox virus (MPXV) is a causative agent of the zoonotic viral disease, human monkeypox (HMPX). MPXV belongs to the genus Orthopoxviridae, a family of notorious smallpox viruses, and so it shares similar clinical pathophysiological features. The recent multicountry HMPX outbreak (May 2022 onwards) is recognized as an emerging global public health emergency by the World Health Organization, shunting its endemic status as opined over the past few decades. Re-emergence of HMPX raises concern to reassess the present clinical strategy and therapeutics as its outbreak evolves further. Keeping a check on these developments, here we provide insights into the HMPX epidemiology, pathophysiology, and clinical representation. Weighing on its early prevention, we reviewed the strategies that are being enrolled for HMPX diagnosis. In the line of expanded MPXV prevalence, we further reviewed its clinical management and the diverse employed preventive/therapeutic strategies, including vaccines (JYNNEOS, ACAM2000, VIGIV) and antiviral drugs/inhibitors (Tecovirimat, Cidofovir, Brincidofovir). Taken together, with a revised perspective of HMPX re-emergence, the present report summarizes new knowledge on its prevalence, pathology, and prevention strategies.
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Affiliation(s)
- Nilanjan Ghosh
- Molecular Pharmacology Research Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, West Bengal, India
| | - Leena Chacko
- BioAnalytical Laboratory, Meso Scale Discovery, Rockville, MD 20850-3173, USA
| | | | - Tanmoy Banerjee
- Molecular Pharmacology Research Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, West Bengal, India
| | - Chandrima Sarkar
- Advanced Pharmacognosy Research Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, West Bengal, India
| | - Birbal Singh
- ICAR-Indian Veterinary Research Institute (IVRI), Regional Station, Palampur 176061, Himachal Pradesh, India
| | - Rajkumar Singh Kalra
- Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| | - Jasvinder Singh Bhatti
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda 151001, Punjab, India
| | - Ramesh Kandimalla
- Department of Biochemistry, Kakatiya Medical College, Warangal 506007, Telangana, India
| | - Saikat Dewanjee
- Advanced Pharmacognosy Research Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, West Bengal, India
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Souiai O, Sallemi A. Retrospective Phylodynamic and Phylogeographic Analysis of the Human Papillomavirus 16 E6 Gene in the Mediterranean Region. Bioinform Biol Insights 2023; 17:11779322231178598. [PMID: 37313033 PMCID: PMC10259103 DOI: 10.1177/11779322231178598] [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: 02/06/2023] [Accepted: 05/11/2023] [Indexed: 06/15/2023] Open
Abstract
Human papillomavirus 16 (HPV16) is considered to be strongly correlated with the development of cervical cancer. Among the 8 HPV16 genes, the E6 constitutes a remarkable marker to follow the evolutionary history and spatial phylodynamics of HPV16 in the Mediterranean basin. Thus, this work aims to decipher the major evolutionary events and crosstalks in the Mediterranean basin with a focus on Tunisian strains regarding the E6 oncogene. In this study, we first extracted the available and annotated Mediterranean strains of HPV16 E6 gene sequences (n = 155) from the NCBI nucleotide database. These sequences were aligned, edited, and used for the downstream phylogenetic analyses. Finally, a Bayesian Markov Chain Monte Carlo approach was applied to reconstruct the evolutionary history of HPV16 migration. Our results showed that the HPV circulating in Tunisia derived from a Croatian ancestor around the year 1987. This starting point spreads to most European countries to reach northern Africa through the Moroccan gateway in 2004.
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Affiliation(s)
- Oussama Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Ameni Sallemi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Institut Pasteur de Tunis, Tunis, Tunisia
- Institut Supérieur de Biotechnologie de Sidi Thabet, Ariana, Tunisia
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30
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Pereson MJ, Sanabria DJ, Torres C, Liotta DJ, Campos RH, Schurr TG, Di Lello FA, Badano I. Evolutionary analysis of JC polyomavirus in Misiones' population yields insight into the population dynamics of the early human dispersal in the Americas. Virology 2023; 585:100-108. [PMID: 37327595 DOI: 10.1016/j.virol.2023.05.009] [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: 03/14/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND JC polyomavirus (JCV) has an ethno-geographical distribution across human populations. OBJECTIVE Study the origins of the population of Misiones (Argentina) by using JCV as genetic marker. METHODS Viral detection and characterization was conducted by PCR amplification and evolutionary analysis of the intergenic region sequences. RESULTS 22 out of 121 samples were positive for JCV, including 5 viral lineages: MY (n = 8), Eu-a (n = 7), B1-c (n = 4), B1-b (n = 2) and Af2 (n = 1). MY sequences clustered within a branch of Native American origin that diverged from its Asian counterpart about 21,914 years ago (HPD 95% interval 15,383-30,177), followed by a sustained demographic expansion around 5000 years ago. CONCLUSIONS JCV in Misiones reflects the multiethnic origin of the current population, with an important Amerindian contribution. Analysis of the MY viral lineage shows a pattern consistent with the arrival of early human migrations to the Americas and a population expansion by the pre-Columbian native societies.
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Affiliation(s)
- Matias J Pereson
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina
| | - Daiana J Sanabria
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina; Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Laboratorio de Biología Molecular Aplicada (LaBiMAp). Posadas, Misiones, Argentina
| | - Carolina Torres
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina
| | - Domingo J Liotta
- Instituto Nacional de Medicina Tropical-ANLIS ''Dr. Malbrán'', Neuquén y Jujuy S/n, N3370, Puerto Iguazú, Misiones, Argentina
| | - Rodolfo H Campos
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina
| | - Theodore G Schurr
- Laboratory of Molecular Anthropology, Department of Anthropology, University of Pennsylvania. Philadelphia, PA 19104-6398, USA
| | - Federico A Di Lello
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina
| | - Inés Badano
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina; Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Laboratorio de Biología Molecular Aplicada (LaBiMAp). Posadas, Misiones, Argentina; Universidad Nacional de Misiones. Red de Laboratorios. Laboratorio de Antropología Biológica y Bioinformática Aplicada (LABBA). Misiones, Argentina.
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31
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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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Nasrin T, Hoque M, Ali S. Systems biology of the genomes' microsatellite signature of Orthopoxvirus including the Monkeypox virus. Comp Immunol Microbiol Infect Dis 2023; 98:102002. [PMID: 37329681 DOI: 10.1016/j.cimid.2023.102002] [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: 12/15/2022] [Revised: 05/07/2023] [Accepted: 05/30/2023] [Indexed: 06/19/2023]
Abstract
This study is an attempt to extract and analyse the microsatellites or simple sequence repeats (SSRs) from the genomes of eight species of the genus Orthopoxvirus. The average size of genomes included in the study was 205 kb while the GC% was 33% for all but one. A total of 10,584 SSRs and 854 cSSRs were observed. POX2 with the largest genome of 224.499 kb had maximum of 1493 SSRs and 121 cSSRs (compound SSR) while POX7 with the smallest genome of 185.578 kb had minimum incident SSRs and cSSRs at 1181 and 96, respectively. There was significant correlation between genome size and SSR incidence. Di-nucleotide repeats were the most prevalent (57.47%) followed by mono- at 33% and tri- at 8.6%. Mono-nucleotide SSRs were predominantly T (51%) and A (48.4%). A majority of 80.32% SSRs were in the coding region. The three most similar genomes as per heat map POX1, POX7 and POX5 (93% similarity) are adjacent to one another in the phylogenetic tree. Ankyrin/Ankyrin like protein and Kelch protein which are associated with host determination and divergence have the highest SSR density in almost all studied viruses. Thus, SSRs are involved in genome evolution and host determination of viruses.
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Affiliation(s)
- Taslima Nasrin
- Clinical and Applied Genomics (CAG) Laboratory Department of Biological Sciences, Aliah University, Kolkata, India
| | - Mehboob Hoque
- Applied Biochemistry Laboratory, Department of Biological Sciences, Aliah University, Kolkata, India
| | - Safdar Ali
- Clinical and Applied Genomics (CAG) Laboratory Department of Biological Sciences, Aliah University, Kolkata, India.
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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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35
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Abdelaal A, Reda A, Hassan AR, Mashaal A, Abu Serhan H, Katamesh BE, Abdelazeem B, Mohanty A, Padhi BK, Rodriguez-Morales AJ, Sah R. Monkeypox-Associated Manifestations and Complications Involving the Eye: A Systematic Review and Meta-Analysis of Previous and Current Outbreaks. Asia Pac J Ophthalmol (Phila) 2023; 12:326-337. [PMID: 37249903 DOI: 10.1097/apo.0000000000000608] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/13/2023] [Indexed: 05/31/2023] Open
Abstract
PURPOSE The purpose of this study was to pool the prevalence rate of monkeypox-associated eye manifestations and/or complications during the current and previous outbreaks. DESIGN A systematic review and meta-analysis. MATERIALS AND METHODS On August 7, 2022, PubMed, Scopus, Web of Science, EMBASE, and Google Scholar were searched for relevant articles. We included all studies that reported the involvement of the eye (either as a manifestation or a complication) among patients with monkeypox. The primary outcome included pooling the effect size (ES) of reported manifestations and complications, and the secondary outcome included the conduct of a subgroup analysis based on the timing of the monkeypox outbreak (before vs. during 2022). RESULTS Eleven studies reporting 3179 monkeypox-confirmed cases were included. Eye manifestations included conjunctivitis, corneal, conjunctival, and eyelid lesions, photophobia, and eye pain. Compared with previous monkeypox outbreaks, the current outbreak revealed much lower rates of ocular involvement in terms of conjunctivitis (ES=1%; 95% CI: 0%-1% vs. ES=17%; 95% CI: 11%-22%), corneal and conjunctival lesions (ES=1%; 95% CI: 0%-2% vs. ES=13%; 95% CI: 4%-22%), and eyelid lesions (ES=1%; 95% CI: 0%-4% vs. ES=13%; 95% CI: 5%-28%). Monkeypox-associated eye complications were reported only in the previous outbreaks which included keratitis (ES=4%; 95% CI: 3%-6%), corneal ulceration (ES=4%; 95% CI: 2%-5%), unilateral (ES=3%; 95% CI: 1%-4%) and bilateral blindness (ES=0%; 95% CI: 0%-2%), and impaired vision (ES=4%; 95% CI: 1%-8%). CONCLUSIONS Ophthalmic manifestations and complications are common among monkeypox-confirmed cases. Although these data are mainly related to previous outbreaks, health care workers should familiarize themselves with these signs to provide better care for monkeypox patients.
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Affiliation(s)
- Abdelaziz Abdelaal
- Tanta Research Team, Tanta, El-Gharbia Governorate, Egypt
- Harvard Medical School, Boston, MA, US
- Boston University School of Medicine, Boston, MA, US
- Doheny Eye Institute, University of California, Los Angeles, Los Angeles, CA, US
- Faculty of Medicine, Tanta University, Tanta, El-Gharbia Governorate, Egypt
| | - Abdullah Reda
- Faculty of Medicine, Al-Azhar University, Cairo, Egypt
| | - Abdul Rhman Hassan
- Tanta Research Team, Tanta, El-Gharbia Governorate, Egypt
- Faculty of Medicine, Tanta University, Tanta, El-Gharbia Governorate, Egypt
| | - Abdelhafeez Mashaal
- Tanta Research Team, Tanta, El-Gharbia Governorate, Egypt
- Faculty of Medicine, Tanta University, Tanta, El-Gharbia Governorate, Egypt
| | - Hashem Abu Serhan
- Tanta Research Team, Tanta, El-Gharbia Governorate, Egypt
- Department of Ophthalmology, Hamad Medical Corporations, Doha, Qatar
| | - Basant E Katamesh
- Tanta Research Team, Tanta, El-Gharbia Governorate, Egypt
- Faculty of Medicine, Tanta University, Tanta, El-Gharbia Governorate, Egypt
- Mayo Clinic, Rochester, MN, US
| | - Basel Abdelazeem
- McLaren Health Care, Flint, Michigan, US
- Michigan State University, East Lansing, Michigan, US
| | - Aroop Mohanty
- All India Institute of Medical Sciences, Gorakhpur, Uttar Pradesh, India
| | - Bijaya K Padhi
- Department of Community Medicine and School of Public Health, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Alfonso J Rodriguez-Morales
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Master's Program of Clinical Epidemiology and Biostatistics, Scientific University of the South (Universidad Científica del Sur), Lima, Peru
| | - Ranjit Sah
- Tribhuvan University Teaching Hospital, Institute of Medicine, Kathmandu, Nepal
- Department of Microbiology, Dr. D.Y. Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pune, Maharashtra, India
- Department of Public Health Dentistry, Dr. D.Y. Patil Dental College and Hospital, Dr. D.Y. Patil Vidyapeeth, Pune, Maharashtra, India
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36
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Yu X, Shi H, Cheng G. Mpox Virus: Its Molecular Evolution and Potential Impact on Viral Epidemiology. Viruses 2023; 15:v15040995. [PMID: 37112975 PMCID: PMC10142743 DOI: 10.3390/v15040995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/15/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Mpox (previously known as monkeypox) is an infectious viral illness caused by the mpox virus (MPXV), an orthopoxvirus that belongs to the family Poxviridae. The symptoms of mpox in humans are similar to those of smallpox, although the mortality rate is lower. In recent years, the concern over a potential global pandemic has increased due to reports of mpox spreading across Africa and other parts of the world. Prior to this discovery, mpox was a rare zoonotic disease restricted to endemic regions of Western and Central Africa. The sudden emergence of MPXV cases in multiple regions has raised concerns about its natural evolution. This review aims to provide an overview of previously available information about MPXV, including its genome, morphology, hosts and reservoirs, and virus-host interaction and immunology, as well as to perform phylogenetic analysis on available MPXV genomes, with an emphasis on the evolution of the genome in humans as new cases emerge.
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Affiliation(s)
- Xi Yu
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen 518000, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Huicheng Shi
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Gong Cheng
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen 518000, China
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
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37
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Veith T, Bleicker T, Eschbach-Bludau M, Brünink S, Mühlemann B, Schneider J, Beheim-Schwarzbach J, Rakotondranary SJ, Ratovonamana YR, Tsagnangara C, Ernest R, Randriantafika F, Sommer S, Stetter N, Jones TC, Drosten C, Ganzhorn JU, Corman VM. Non-structural genes of novel lemur adenoviruses reveal codivergence of virus and host. Virus Evol 2023; 9:vead024. [PMID: 37091898 PMCID: PMC10121206 DOI: 10.1093/ve/vead024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 03/06/2023] [Accepted: 03/27/2023] [Indexed: 03/29/2023] Open
Abstract
Adenoviruses (AdVs) are important human and animal pathogens and are frequently used as vectors for gene therapy and vaccine delivery. Surprisingly, there are only scant data regarding primate AdV origin and evolution, especially in the most basal primate hosts. We detect and sequence AdVs from faeces of two Madagascan lemur species. Complete genome sequence analyses define a new AdV species with a particularly large gene encoding a protein of unknown function in the early gene region 3. Unexpectedly, the new AdV species is not most similar to human or other simian AdVs but to bat adenovirus C. Genome characterisation shows signals of virus-host codivergence in non-structural genes, which show lower diversity than structural genes. Outside a lemur species mixing zone, recombination less frequently separates structural genes, as in human adenovirus C. The evolutionary history of lemur AdVs likely involves both a host switch and codivergence with the lemur hosts.
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Affiliation(s)
- Talitha Veith
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
| | - Tobias Bleicker
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
| | - Monika Eschbach-Bludau
- Institute of Virology, University Hospital, University of Bonn, Venusberg-Campus 1, Bonn 53127, Germany
| | - Sebastian Brünink
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
| | - Barbara Mühlemann
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
- German Centre for Infection Research (DZIF), Partner Site Berlin, Charitéplatz 1, Berlin 10117, Germany
| | - Julia Schneider
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
- German Centre for Infection Research (DZIF), Partner Site Berlin, Charitéplatz 1, Berlin 10117, Germany
| | - Jörn Beheim-Schwarzbach
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
| | - S Jacques Rakotondranary
- Institute of Cell and Systems Biology of Animals, Universität Hamburg, Martin-Luther-King Platz 3, Hamburg 20146, Germany
- Département Biologie Animale, Faculté des Sciences, Université d’ Antananarivo, P.O. Box 906, Antananarivo 101, Madagascar
| | - Yedidya R Ratovonamana
- Institute of Cell and Systems Biology of Animals, Universität Hamburg, Martin-Luther-King Platz 3, Hamburg 20146, Germany
- Département Biologie Animale, Faculté des Sciences, Université d’ Antananarivo, P.O. Box 906, Antananarivo 101, Madagascar
| | - Cedric Tsagnangara
- Tropical Biodiversity and Social Enterprise SARL, Immeuble CNAPS, premier étage, Fort Dauphin 614, Madagascar
| | - Refaly Ernest
- Tropical Biodiversity and Social Enterprise SARL, Immeuble CNAPS, premier étage, Fort Dauphin 614, Madagascar
| | | | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein Allee 11, Ulm 89069, Germany
| | - Nadine Stetter
- Institute of Cell and Systems Biology of Animals, Universität Hamburg, Martin-Luther-King Platz 3, Hamburg 20146, Germany
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, Hamburg 20359, Germany
| | - Terry C Jones
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
- German Centre for Infection Research (DZIF), Partner Site Berlin, Charitéplatz 1, Berlin 10117, Germany
| | - Jörg U Ganzhorn
- Institute of Cell and Systems Biology of Animals, Universität Hamburg, Martin-Luther-King Platz 3, Hamburg 20146, Germany
| | - Victor M Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
- German Centre for Infection Research (DZIF), Partner Site Berlin, Charitéplatz 1, Berlin 10117, Germany
- Labor Berlin, Charité—Vivantes GmbH, Sylter Straße 2, Berlin 13353, Germany
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38
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de-Dios T, Scheib CL, Houldcroft CJ. An Adagio for Viruses, Played Out on Ancient DNA. Genome Biol Evol 2023; 15:evad047. [PMID: 36930529 PMCID: PMC10063219 DOI: 10.1093/gbe/evad047] [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: 12/05/2022] [Revised: 02/16/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
Studies of ancient DNA have transformed our understanding of human evolution. Paleogenomics can also reveal historic and prehistoric agents of disease, including endemic, epidemic, and pandemic pathogens. Viruses-and in particular those with single- or double-stranded DNA genomes-are an important part of the paleogenomic revolution, preserving within some remains or environmental samples for tens of thousands of years. The results of these studies capture the public imagination, as well as giving scientists a unique perspective on some of the more slowly evolving viruses which cause disease. In this review, we revisit the first studies of historical virus genetic material in the 1990s, through to the genomic revolution of recent years. We look at how paleogenomics works for viral pathogens, such as the need for careful precautions against modern contamination and robust computational pipelines to identify and analyze authenticated viral sequences. We discuss the insights into virus evolution which have been gained through paleogenomics, concentrating on three DNA viruses in particular: parvovirus B19, herpes simplex virus 1, and smallpox. As we consider recent worldwide transmission of monkeypox and synthetic biology tools that allow the potential reconstruction of extinct viruses, we show that studying historical and ancient virus evolution has never been more topical.
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Affiliation(s)
- Toni de-Dios
- Institute of Genomics, University of Tartu, Estonia
| | - Christiana L Scheib
- Institute of Genomics, University of Tartu, Estonia
- St. John's College, University of Cambridge, United Kingdom
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39
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Guan H, Gul I, Xiao C, Ma S, Liang Y, Yu D, Liu Y, Liu H, Zhang CY, Li J, Qin P. Emergence, phylogeography, and adaptive evolution of mpox virus. New Microbes New Infect 2023; 52:101102. [PMID: 36815201 PMCID: PMC9937731 DOI: 10.1016/j.nmni.2023.101102] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023] Open
Abstract
Mpox (Monkeypox) is a zoonotic disease caused by mpox virus (MPXV). A multi-country MPXV outbreak in non-endemic demographics was identified in May 2022. A systematic evaluation of MPXV evolutionary trajectory and genetic diversity could be a timely addition to the MPXV diagnostics and prophylaxis. Herein, we integrated a systematic evolution analysis including phylogenomic and phylogeographic, followed by an in-depth analysis of the adaptive evolution and amino acid variations in type I interferon binding protein (IFNα/βBP). Mutations in IFNα/βBP protein may impair its binding capacity, affecting the MPXV immune evasion strategy. Based on the equilibrated data, we found an evolutionary rate of 7.75 × 10 - 5 substitutions/site/year, and an earlier original time (2021.25) of the clade IIb. We further discovered significant genetic variations in MPXV genomes from different regions and obtained six plausible spread trajectories from its intricate viral flow network, implying that North America might have acted as a bridge for the spread of MPXV from Africa to other continents. We identified two amino acids under positive selection in the Rifampicin resistance protein and extracellular enveloped virus (EEV) type-I membrane glycoprotein, indicating a role in adaptive evolution. Our research sheds light on the emergence, dispersal, and adaptive evolution of MPXV, providing theoretical support for mitigating and containing its expansion.
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Affiliation(s)
- Haifei Guan
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Ijaz Gul
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Chufan Xiao
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Shuyue Ma
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Yingshan Liang
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Dongmei Yu
- School of Mechanical, Electrical & Information Engineering, Shandong University, Weihai, Shandong, 264209, China
| | - Ying Liu
- Food Inspection & Quarantine Center, Shenzhen Custom, Shenzhen, Guangdong, 518060, China
| | - Hong Liu
- Food Inspection & Quarantine Center, Shenzhen Custom, Shenzhen, Guangdong, 518060, China
| | - Can Yang Zhang
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Juan Li
- Advanced Research Institute for Multidisciplinary Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Peiwu Qin
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
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40
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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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41
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Zovi A, Ferrara F, Sorrentino S, Langella R, Trama U, Boccellino M, Vitiello A. 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] [MESH Headings] [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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Affiliation(s)
- Andrea Zovi
- Ministry of Health, Viale Giorgio Ribotta 5, 00144, Rome, Italy
| | - Francesco Ferrara
- Pharmaceutical Department, Asl Napoli 3 Sud, Dell'amicizia street 22, 80035, Nola, Naples, Italy.
| | - Sarah Sorrentino
- Pharmaceutical Department, Asl Napoli 3 Sud, Dell'amicizia street 22, 80035, Nola, Naples, Italy
| | - Roberto Langella
- Italian Society of Hospital Pharmacy (SIFO), SIFO Secretariat of the Lombardy Region, Via Carlo Farini, 81, 20159, Milan, Italy
| | - Ugo Trama
- Health Protection and Coordination of the Campania Regional Health System, Naples, Italy
| | - Mariarosaria Boccellino
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Antonio Vitiello
- Clinical pharmacologist, Ministry of Health, Viale Giorgio Ribotta 5, 00144, Rome, Italy
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42
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Wang L, Shang J, Weng S, Aliyari SR, Ji C, Cheng G, Wu A. Genomic annotation and molecular evolution of monkeypox virus outbreak in 2022. J Med Virol 2023; 95:e28036. [PMID: 35906185 PMCID: PMC10087776 DOI: 10.1002/jmv.28036] [Citation(s) in RCA: 70] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 01/11/2023]
Abstract
Monkeypox virus (MPXV) has generally circulated in West and Central Africa since its emergence. Recently, sporadic MPXV infections in several nonendemic countries have attracted widespread attention. Here, we conducted a systematic analysis of the recent outbreak of MPXV-2022, including its genomic annotation and molecular evolution. The phylogenetic analysis indicated that the MPXV-2022 strains belong to the same lineage of the MPXV strain isolated in 2018. However, compared with the MPXV strain in 2018, in total 46 new consensus mutations were observed in the MPXV-2022 strains, including 24 nonsynonymous mutations. By assigning mutations to 187 proteins encoded by the MPXV genome, we found that 10 proteins in the MPXV are more prone to mutation, including D2L-like, OPG023, OPG047, OPG071, OPG105, OPG109, A27L-like, OPG153, OPG188, and OPG210 proteins. In the MPXV-2022 strains, four and three nucleotide substitutions are observed in OPG105 and OPG210, respectively. Overall, our studies illustrated the genome evolution of the ongoing MPXV outbreak and pointed out novel mutations as a reference for further studies.
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Affiliation(s)
- Lulan Wang
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Jingzhe Shang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, China
| | - Shenghui Weng
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, China
| | - Saba R Aliyari
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Chengyang Ji
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, China
| | - Genhong Cheng
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Aiping Wu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, China
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43
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Lim CK, Roberts J, Moso M, Liew KC, Taouk ML, Williams E, Tran T, Steinig E, Caly L, Williamson DA. Mpox diagnostics: Review of current and emerging technologies. J Med Virol 2023; 95:e28429. [PMID: 36571266 PMCID: PMC10108241 DOI: 10.1002/jmv.28429] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/12/2022] [Accepted: 12/21/2022] [Indexed: 12/27/2022]
Abstract
Mpox is a zoonotic disease caused by monkeypox virus (MPXV) from the Orthopoxvirus genus. Unprecedented transmission events have led to more than 70 000 cases reported worldwide by October 2022. The change in mpox epidemiology has raised concerns of its ability to establish endemicity beyond its traditional geographical locations. In this review, we discuss the current understanding of mpox virology and viral dynamics that are relevant to mpox diagnostics. A synopsis of the traditional and emerging laboratory technologies useful for MPXV detection and in guiding "elimination" strategies is outlined in this review. Importantly, development in MPXV genomics has rapidly advanced our understanding of the role of viral evolution and adaptation in the current outbreak.
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Affiliation(s)
- Chuan Kok Lim
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jason Roberts
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Michael Moso
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Kwee Chin Liew
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Mona L Taouk
- Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Eloise Williams
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas Tran
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Eike Steinig
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Leon Caly
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Deborah Ann Williamson
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
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44
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Davidson I. Avian Oncogenic and Immunosuppressive Viruses. Infect Dis (Lond) 2023. [DOI: 10.1007/978-1-0716-2463-0_1091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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45
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Kumar S, Subramaniam G, Karuppanan K. Human monkeypox outbreak in 2022. J Med Virol 2023; 95:e27894. [PMID: 35637363 DOI: 10.1002/jmv.27894] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 01/11/2023]
Affiliation(s)
- Suresh Kumar
- Department of Diagnostic & Allied Health Science, Faculty of Health and Life Sciences, Management and Science University, ShahAlam, Selangor, Malaysia
| | | | - Kalimuthu Karuppanan
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
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46
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Bragazzi NL, Kong JD, Wu J. Integrated epidemiological, clinical, and molecular evidence points to an earlier origin of the current monkeypox outbreak and a complex route of exposure. J Med Virol 2023; 95:e28244. [PMID: 36261876 DOI: 10.1002/jmv.28244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 01/11/2023]
Affiliation(s)
- Nicola Luigi Bragazzi
- Department of Mathematics and Statistics, Laboratory for Industrial and Applied Mathematics (LIAM), York University, Toronto, Ontario, Canada
| | - Jude D Kong
- Department of Mathematics and Statistics, Laboratory for Industrial and Applied Mathematics (LIAM), York University, Toronto, Ontario, Canada
| | - Jianhong Wu
- Department of Mathematics and Statistics, Laboratory for Industrial and Applied Mathematics (LIAM), York University, Toronto, Ontario, Canada
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47
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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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48
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Sukhdeo S, Mishra S, Walmsley S. Human monkeypox: a comparison of the characteristics of the new epidemic to the endemic disease. BMC Infect Dis 2022; 22:928. [PMID: 36503476 PMCID: PMC9742013 DOI: 10.1186/s12879-022-07900-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/25/2022] [Indexed: 12/14/2022] Open
Abstract
In May 2022, a new global outbreak of mpox (formerly, human monkeypox) emerged that was declared a public health emergency of international concern by the World Health Organization on July 23, 2022. With new patterns of person-to-person spread within sexual networks in nonendemic countries and several differences from the classic disease course, we performed a comprehensive review of existing literature on human monkeypox to discuss epidemiology, modes of transmission, clinical presentation and asymptomatic infection, diagnostics, therapeutics, and vaccines with the primary aim to identify important areas for future research of this new epidemic form of the disease. A comprehensive literature search was performed of all published literature to August 15, 2022. Historically, in regions of monkeypox virus endemicity, human outbreaks have occurred related to discrete zoonotic events. The animal reservoir is unknown, but the virus has been isolated from rodents. Traditionally, transmission occurred by direct or indirect contact with an infected animal. In nonendemic countries affected in the 2022 outbreak, almost exclusive person-to-person spread has been observed, and most cases are connected to sexual networks of gay, bisexual, and other men who have sex with men. After an incubation period of approximately 13 days, in traditional human cases affected persons developed a febrile prodrome preceding a rash that started on the face and body, spread centrifugally to the palms and soles and healed monomorphically over two to four weeks. However, in the 2022 outbreak, the febrile illness is often absent or occurs after the onset of the rash. The rash presents primarily in the anogenital region and face before disseminating throughout the body, with lesions displaying regional pleomorphism. There is a paucity of data for the role of antiviral agents or vaccines. The epidemiology and clinical course of mpox has changed in the 2022 epidemic from that observed with the endemic disease. There is an urgent need to establish rapid and collaborative research platforms to diagnose, treat and prevent disease and inform important public health and other strategies to stop the spread of disease.
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Affiliation(s)
- Sharon Sukhdeo
- Department of Medicine, University of Toronto, Toronto, Canada.
| | - Sharmistha Mishra
- Division of Infectious Diseases, Department of Medicine, St. Michael's Hospital, MAP Centre for Urban Health Solutions, University of Toronto, Toronto, Canada
| | - Sharon Walmsley
- Department of Medicine, Division of Infectious Diseases, University Health Network, University of Toronto, Toronto, Canada
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49
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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: 99] [Impact Index Per Article: 49.5] [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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50
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Dashraath P, Nielsen-Saines K, Rimoin A, Mattar CNZ, Panchaud A, Baud D. Monkeypox in pregnancy: virology, clinical presentation, and obstetric management. Am J Obstet Gynecol 2022; 227:849-861.e7. [PMID: 35985514 PMCID: PMC9534101 DOI: 10.1016/j.ajog.2022.08.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/11/2022] [Accepted: 08/11/2022] [Indexed: 01/26/2023]
Abstract
The 2022 monkeypox outbreak, caused by the zoonotic monkeypox virus, has spread across 6 World Health Organization regions (the Americas, Africa, Europe, Eastern Mediterranean, Western Pacific, and South-East Asia) and was declared a public health emergency of international concern on July 23, 2022. The global situation is especially concerning given the atypically high rate of person-to-person transmission, which suggests viral evolution to an established human pathogen. Pregnant women are at heightened risk of vertical transmission of the monkeypox virus because of immune vulnerability and natural depletion of population immunity to smallpox among reproductive-age women, and because orthopoxviral cell entry mechanisms can overcome the typically viral-resistant syncytiotrophoblast barrier within the placenta. Data on pregnancy outcomes following monkeypox infection are scarce but include reports of miscarriage, intrauterine demise, preterm birth, and congenital infection. This article forecasts the issues that maternity units might face and proposes guidelines to protect the health of pregnant women and fetuses exposed to the monkeypox virus. We review the pathophysiology and clinical features of monkeypox infection and discuss the obstetrical implications of the unusually high prevalence of anogenital lesions. We describe the use of real-time polymerase chain reaction tests from mucocutaneous and oropharyngeal sites to confirm infection, and share an algorithm for the antenatal management of pregnant women with monkeypox virus exposure. On the basis of the best available knowledge from prenatal orthopoxvirus infections, we discuss the sonographic features of congenital monkeypox and the role of invasive testing in establishing fetal infection. We suggest a protocol for cesarean delivery to avoid the horizontal transmission of the monkeypox virus at birth and address the controversy of mother-infant separation in the postpartum period. Obstetrical concerns related to antiviral therapy with tecovirimat and vaccinia immune globulin are highlighted, including the risks of heart rate-corrected QT-interval prolongation, inaccuracies in blood glucose monitoring, and the predisposition to iatrogenic venous thromboembolism. The possibility of monkeypox vaccine hesitancy during pregnancy is discussed, and strategies are offered to mitigate these risks. Finally, we conclude with a research proposal to address knowledge gaps related to the impact of monkeypox infection on maternal, fetal, and neonatal health.
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Affiliation(s)
- Pradip Dashraath
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, National University Hospital, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
| | - Karin Nielsen-Saines
- Division of Pediatric Infectious Diseases, Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Anne Rimoin
- Fielding School of Public Health, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA; University of California Los Angeles-Democratic Republic of the Congo Health Research and Training Program, Kinshasa, Democratic Republic of the Congo
| | - Citra N Z Mattar
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, National University Hospital, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Alice Panchaud
- Institute of Primary Health Care (BIHAM), University of Bern, Bern, Switzerland
| | - David Baud
- Materno-fetal and Obstetrics Research Unit, Department Woman-Mother-Child, Lausanne University Hospital, Lausanne, Switzerland
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