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Natasha A, Pye SE, Park K, Rajoriya S, Yang I, Park J, Pangestu HS, Kim J, Oh Y, López CB, Song JW, Kim WK. Detection and characterization of Langya virus in Crocidura lasiura , Republic of Korea. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.02.626520. [PMID: 39677782 PMCID: PMC11642890 DOI: 10.1101/2024.12.02.626520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
Abstract
This study reports the identification of Langya virus Korea (LayV KOR) during the surveillance of shrews in the Republic of Korea. LayV KOR represents the first identification of LayV outside of China, exhibiting approximately 80% and 95.5% homologies at nucleotide and amino acid levels.
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Yan C, Zhou W, Zhang Y, Zhou X, Qiao Q, Miao L, Xu Z. Super-Resolution Imaging Reveals the Mechanism of Endosomal Acidification Inhibitors Against SARS-CoV-2 Infection. Chembiochem 2024; 25:e202400404. [PMID: 38877380 DOI: 10.1002/cbic.202400404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/14/2024] [Accepted: 06/14/2024] [Indexed: 06/16/2024]
Abstract
In this study, super-resolution structured illumination microscope (SIM) was used to analyze molecular mechanism of endocytic acidification inhibitors in the SARS-CoV-2 pandemic, such as Chloroquine (CQ), Hydroxychloroquine (HCQ) and Bafilomycin A1 (BafA1). We fluorescently labeled the SARS-CoV-2 RBD and its receptor ACE2 protein with small molecule dyes. Utilizing SIM imaging, the real-time impact of inhibitors (BafA1, CQ, HCQ, Dynasore) on the RBD-ACE2 endocytotic process was dynamically tracked in living cells. Initially, the protein activity of RBD and ACE2 was ensured after being labeled. And then our findings revealed that these inhibitors could inhibit the internalization and degradation of RBD-ACE2 to varying degrees. Among them, 100 nM BafA1 exhibited the most satisfactory endocytotic inhibition (~63.9 %) and protein degradation inhibition (~97.7 %). And it could inhibit the fusion between endocytic vesicles in the living cells. Additionally, Dynasore, a widely recognized dynein inhibitor, also demonstrated cell acidification inhibition effects. Together, these inhibitors collectively hinder SARS-CoV-2 infection by inhibiting both the viral internalization and RNA release. The comprehensive evaluation of pharmacological mechanisms through super-resolution fluorescence imaging has laid a crucial theoretical foundation for the development of potential drugs to treat COVID-19.
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Affiliation(s)
- Chunyu Yan
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
- School of Chemistry, Dalian University of Technology, 2 Linggong Road, Dalian, 116024, China
| | - Wei Zhou
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Yan Zhang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
- School of Chemistry, Dalian University of Technology, 2 Linggong Road, Dalian, 116024, China
| | - Xuelian Zhou
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
- School of Chemistry, Dalian University of Technology, 2 Linggong Road, Dalian, 116024, China
| | - Qinglong Qiao
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Lu Miao
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Zhaochao Xu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
- School of Chemistry, Dalian University of Technology, 2 Linggong Road, Dalian, 116024, China
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Tramuto F, Maida CM, Randazzo G, Guzzetta V, Santino A, Li Muli R, Costantino C, Graziano G, Amodio E, Mazzucco W, Vitale F. Whole-Genome Sequencing and Genetic Diversity of Human Respiratory Syncytial Virus in Patients with Influenza-like Illness in Sicily (Italy) from 2017 to 2023. Viruses 2024; 16:851. [PMID: 38932144 PMCID: PMC11209242 DOI: 10.3390/v16060851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
Monitoring the genetic variability of human respiratory syncytial virus (hRSV) is of paramount importance, especially for the potential implication of key antigenic mutations on the emergence of immune escape variants. Thus, to describe the genetic diversity and evolutionary dynamics of hRSV circulating in Sicily (Italy), a total of 153 hRSV whole-genome sequences collected from 770 hRSV-positive subjects between 2017 and 2023, before the introduction of expanded immunization programs into the population, were investigated. The phylogenetic analyses indicated that the genotypes GA.2.3.5 (ON1) for hRSV-A and GB.5.0.5a (BA9) for hRSV-B co-circulated in our region. Amino acid (AA) substitutions in the surface and internal proteins were evaluated, including the F protein antigenic sites, as the major targets of immunoprophylactic monoclonal antibodies and vaccines. Overall, the proportion of AA changes ranged between 1.5% and 22.6% among hRSV-A, whereas hRSV-B varied in the range 0.8-16.9%; the latter was more polymorphic than hRSV-A within the key antigenic sites. No AA substitutions were found at site III of both subgroups. Although several non-synonymous mutations were found, none of the polymorphisms known to potentially affect the efficacy of current preventive measures were documented. These findings provide new insights into the global hRSV molecular epidemiology and highlight the importance of defining a baseline genomic picture to monitor for future changes that might be induced by the selective pressures of immunological preventive measures, which will soon become widely available.
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Affiliation(s)
- Fabio Tramuto
- Department of Health Promotion Sciences Maternal and Infant Care, Internal Medicine and Medical Specialties “G. D’Alessandro”—Hygiene Section, University of Palermo, 90133 Palermo, Italy; (C.M.M.); (C.C.); (E.A.); (W.M.); (F.V.)
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Carmelo Massimo Maida
- Department of Health Promotion Sciences Maternal and Infant Care, Internal Medicine and Medical Specialties “G. D’Alessandro”—Hygiene Section, University of Palermo, 90133 Palermo, Italy; (C.M.M.); (C.C.); (E.A.); (W.M.); (F.V.)
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Giulia Randazzo
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Valeria Guzzetta
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Arianna Santino
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Rita Li Muli
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Claudio Costantino
- Department of Health Promotion Sciences Maternal and Infant Care, Internal Medicine and Medical Specialties “G. D’Alessandro”—Hygiene Section, University of Palermo, 90133 Palermo, Italy; (C.M.M.); (C.C.); (E.A.); (W.M.); (F.V.)
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Giorgio Graziano
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Emanuele Amodio
- Department of Health Promotion Sciences Maternal and Infant Care, Internal Medicine and Medical Specialties “G. D’Alessandro”—Hygiene Section, University of Palermo, 90133 Palermo, Italy; (C.M.M.); (C.C.); (E.A.); (W.M.); (F.V.)
| | - Walter Mazzucco
- Department of Health Promotion Sciences Maternal and Infant Care, Internal Medicine and Medical Specialties “G. D’Alessandro”—Hygiene Section, University of Palermo, 90133 Palermo, Italy; (C.M.M.); (C.C.); (E.A.); (W.M.); (F.V.)
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Francesco Vitale
- Department of Health Promotion Sciences Maternal and Infant Care, Internal Medicine and Medical Specialties “G. D’Alessandro”—Hygiene Section, University of Palermo, 90133 Palermo, Italy; (C.M.M.); (C.C.); (E.A.); (W.M.); (F.V.)
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
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Balasco N, Damaggio G, Esposito L, Colonna V, Vitagliano L. A comprehensive analysis of SARS-CoV-2 missense mutations indicates that all possible amino acid replacements in the viral proteins occurred within the first two-and-a-half years of the pandemic. Int J Biol Macromol 2024; 266:131054. [PMID: 38522702 DOI: 10.1016/j.ijbiomac.2024.131054] [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: 01/25/2024] [Revised: 02/27/2024] [Accepted: 03/08/2024] [Indexed: 03/26/2024]
Abstract
The surveillance of COVID-19 pandemic has led to the determination of millions of genome sequences of the SARS-CoV-2 virus, with the accumulation of a wealth of information never collected before for an infectious disease. Exploring the information retrieved from the GISAID database reporting at that time >13 million genome sequences, we classified the 141,639 unique missense mutations detected in the first two-and-a-half years (up to October 2022) of the pandemic. Notably, our analysis indicates that 98.2 % of all possible conservative amino acid replacements occurred. Even non-conservative mutations were highly represented (73.9 %). For a significant number of residues (3 %), all possible replacements with the other nineteen amino acids have been observed. These observations strongly indicate that, in this time interval, the virus explored all possible alternatives in terms of missense mutations for all sites of its polypeptide chain and that those that are not observed severely affect SARS-CoV-2 integrity. The implications of the present findings go well beyond the structural biology of SARS-CoV-2 as the huge amount of information here collected and classified may be valuable for the elucidation of the sequence-structure-function relationships in proteins.
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Affiliation(s)
- Nicole Balasco
- Institute of Molecular Biology and Pathology, CNR c/o Dep. Chemistry, Sapienza University of Rome, Rome, Italy.
| | - Gianluca Damaggio
- Institute of Genetics and Biophysics, CNR, Naples, Italy; Laboratory of Stem Cell Biology and Pharmacology of Neurodegenerative Diseases, Department of Biosciences, University of Milan, Milan, Italy; University of Naples Federico II, Naples, Italy
| | | | - Vincenza Colonna
- Institute of Genetics and Biophysics, CNR, Naples, Italy; Department of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
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5
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Koma T, Doi N, Le BQ, Kondo T, Ishizue M, Tokaji C, Tsukada C, Adachi A, Nomaguchi M. Involvement of a Rarely Used Splicing SD2b Site in the Regulation of HIV-1 vif mRNA Production as Revealed by a Growth-Adaptive Mutation. Viruses 2023; 15:2424. [PMID: 38140666 PMCID: PMC10747208 DOI: 10.3390/v15122424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/09/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
We have previously reported an HIV-1 mutant designated NL-Y226tac that expresses Vif at an ultra-low level, being replication-defective in high-APOBEC3G cells, such as H9. It carries a synonymous mutation within the splicing SA1 site relative to its parental clone. In order to determine whether a certain mutant(s) emerges during multi-infection cycles, we maintained H9 cells infected with a relatively low or high input of NL-Y226tac for extended time periods. Unexpectedly, we reproducibly identified a g5061a mutation in the SD2b site in the two independent long-term culture experiments that partially increases Vif expression and replication ability. Importantly, the adaptive mutation g5061a was demonstrated to enhance vif mRNA production by activation of the SA1 site mediated through increasing usage of a rarely used SD2b site. In the long-term culture initiated by a high virus input, we additionally found a Y226Fttc mutation at the original Y226tac site in SA1 that fully restores Vif expression and replication ability. As expected, the adaptive mutation Y226Fttc enhances vif mRNA production through increasing the splicing site usage of SA1. Our results here revealed the importance of the SD2b nucleotide sequence in producing vif mRNA involved in the HIV-1 adaptation and of mutual antagonism between Vif and APOBEC3 proteins in HIV-1 adaptation/evolution and survival.
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Affiliation(s)
- Takaaki Koma
- Department of Microbiology, Graduate School of Medicine, Tokushima University, Tokushima 770-8503, Japan; (T.K.); (N.D.); (B.Q.L.); (T.K.)
| | - Naoya Doi
- Department of Microbiology, Graduate School of Medicine, Tokushima University, Tokushima 770-8503, Japan; (T.K.); (N.D.); (B.Q.L.); (T.K.)
| | - Bao Quoc Le
- Department of Microbiology, Graduate School of Medicine, Tokushima University, Tokushima 770-8503, Japan; (T.K.); (N.D.); (B.Q.L.); (T.K.)
| | - Tomoyuki Kondo
- Department of Microbiology, Graduate School of Medicine, Tokushima University, Tokushima 770-8503, Japan; (T.K.); (N.D.); (B.Q.L.); (T.K.)
| | - Mitsuki Ishizue
- Department of Microbiology, Graduate School of Medicine, Tokushima University, Tokushima 770-8503, Japan; (T.K.); (N.D.); (B.Q.L.); (T.K.)
- Faculty of Medicine, Tokushima University, Tokushima 770-8503, Japan
| | - Chiaki Tokaji
- Department of Microbiology, Graduate School of Medicine, Tokushima University, Tokushima 770-8503, Japan; (T.K.); (N.D.); (B.Q.L.); (T.K.)
- Faculty of Medicine, Tokushima University, Tokushima 770-8503, Japan
| | - Chizuko Tsukada
- Department of Microbiology, Graduate School of Medicine, Tokushima University, Tokushima 770-8503, Japan; (T.K.); (N.D.); (B.Q.L.); (T.K.)
- Faculty of Medicine, Tokushima University, Tokushima 770-8503, Japan
| | - Akio Adachi
- Department of Microbiology, Graduate School of Medicine, Tokushima University, Tokushima 770-8503, Japan; (T.K.); (N.D.); (B.Q.L.); (T.K.)
| | - Masako Nomaguchi
- Department of Microbiology, Graduate School of Medicine, Tokushima University, Tokushima 770-8503, Japan; (T.K.); (N.D.); (B.Q.L.); (T.K.)
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6
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Rochman ND, Koonin EV. Learn from the past to predict viral pandemics. Nature 2023; 622:700-702. [PMID: 37821603 DOI: 10.1038/d41586-023-02931-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
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7
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Bloom JD, Neher RA. Fitness effects of mutations to SARS-CoV-2 proteins. Virus Evol 2023; 9:vead055. [PMID: 37727875 PMCID: PMC10506532 DOI: 10.1093/ve/vead055] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/08/2023] [Accepted: 08/22/2023] [Indexed: 09/21/2023] Open
Abstract
Knowledge of the fitness effects of mutations to SARS-CoV-2 can inform assessment of new variants, design of therapeutics resistant to escape, and understanding of the functions of viral proteins. However, experimentally measuring effects of mutations is challenging: we lack tractable lab assays for many SARS-CoV-2 proteins, and comprehensive deep mutational scanning has been applied to only two SARS-CoV-2 proteins. Here, we develop an approach that leverages millions of publicly available SARS-CoV-2 sequences to estimate effects of mutations. We first calculate how many independent occurrences of each mutation are expected to be observed along the SARS-CoV-2 phylogeny in the absence of selection. We then compare these expected observations to the actual observations to estimate the effect of each mutation. These estimates correlate well with deep mutational scanning measurements. For most genes, synonymous mutations are nearly neutral, stop-codon mutations are deleterious, and amino acid mutations have a range of effects. However, some viral accessory proteins are under little to no selection. We provide interactive visualizations of effects of mutations to all SARS-CoV-2 proteins (https://jbloomlab.github.io/SARS2-mut-fitness/). The framework we describe is applicable to any virus for which the number of available sequences is sufficiently large that many independent occurrences of each neutral mutation are observed.
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Affiliation(s)
- Jesse D Bloom
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Richard A Neher
- Biozentrum, University of Basel, Spitalstrasse 41, Basel 4056, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerl
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Wasik BR, Rothschild E, Voorhees IEH, Reedy SE, Murcia PR, Pusterla N, Chambers TM, Goodman LB, Holmes EC, Kile JC, Parrish CR. Understanding the divergent evolution and epidemiology of H3N8 influenza viruses in dogs and horses. Virus Evol 2023; 9:vead052. [PMID: 37692894 PMCID: PMC10484056 DOI: 10.1093/ve/vead052] [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: 03/22/2023] [Revised: 06/12/2023] [Accepted: 08/16/2023] [Indexed: 09/12/2023] Open
Abstract
Cross-species virus transmission events can lead to dire public health emergencies in the form of epidemics and pandemics. One example in animals is the emergence of the H3N8 equine influenza virus (EIV), first isolated in 1963 in Miami, FL, USA, after emerging among horses in South America. In the early 21st century, the American lineage of EIV diverged into two 'Florida' clades that persist today, while an EIV transferred to dogs around 1999 and gave rise to the H3N8 canine influenza virus (CIV), first reported in 2004. Here, we compare CIV in dogs and EIV in horses to reveal their host-specific evolution, to determine the sources and connections between significant outbreaks, and to gain insight into the factors controlling their different evolutionary fates. H3N8 CIV only circulated in North America, was geographically restricted after the first few years, and went extinct in 2016. Of the two EIV Florida clades, clade 1 circulates widely and shows frequent transfers between the USA and South America, Europe and elsewhere, while clade 2 was globally distributed early after it emerged, but since about 2018 has only been detected in Central Asia. Any potential zoonotic threat of these viruses to humans can only be determined with an understanding of its natural history and evolution. Our comparative analysis of these three viral lineages reveals distinct patterns and rates of sequence variation yet with similar overall evolution between clades, suggesting epidemiological intervention strategies for possible eradication of H3N8 EIV.
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Affiliation(s)
- Brian R Wasik
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Evin Rothschild
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Ian E H Voorhees
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Stephanie E Reedy
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA
| | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, Scotland
| | - Nicola Pusterla
- Department of Medicine & Epidemiology, School Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Thomas M Chambers
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA
| | - Laura B Goodman
- Baker Institute for Animal Health, Department of Public and Ecosystems Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - James C Kile
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Colin R Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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9
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Biancolella M, Colona VL, Luzzatto L, Watt JL, Mattiuz G, Conticello SG, Kaminski N, Mehrian-Shai R, Ko AI, Gonsalves GS, Vasiliou V, Novelli G, Reichardt JKV. COVID-19 annual update: a narrative review. Hum Genomics 2023; 17:68. [PMID: 37488607 PMCID: PMC10367267 DOI: 10.1186/s40246-023-00515-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/16/2023] [Indexed: 07/26/2023] Open
Abstract
Three and a half years after the pandemic outbreak, now that WHO has formally declared that the emergency is over, COVID-19 is still a significant global issue. Here, we focus on recent developments in genetic and genomic research on COVID-19, and we give an outlook on state-of-the-art therapeutical approaches, as the pandemic is gradually transitioning to an endemic situation. The sequencing and characterization of rare alleles in different populations has made it possible to identify numerous genes that affect either susceptibility to COVID-19 or the severity of the disease. These findings provide a beginning to new avenues and pan-ethnic therapeutic approaches, as well as to potential genetic screening protocols. The causative virus, SARS-CoV-2, is still in the spotlight, but novel threatening virus could appear anywhere at any time. Therefore, continued vigilance and further research is warranted. We also note emphatically that to prevent future pandemics and other world-wide health crises, it is imperative to capitalize on what we have learnt from COVID-19: specifically, regarding its origins, the world's response, and insufficient preparedness. This requires unprecedented international collaboration and timely data sharing for the coordination of effective response and the rapid implementation of containment measures.
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Affiliation(s)
| | - Vito Luigi Colona
- Department of Biomedicine and Prevention, School of Medicine and Surgery, Tor Vergata University of Rome, Via Montpellier 1, 00133, Rome, Italy
| | - Lucio Luzzatto
- Department of Haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- University of Florence, 50121, Florence, Italy
| | - Jessica Lee Watt
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Smithfield, QLD, 4878, Australia
| | | | - Silvestro G Conticello
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Florence, Italy
- Institute of Clinical Physiology - National Council of Research (IFC-CNR), 56124, Pisa, Italy
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Ruty Mehrian-Shai
- Pediatric Hemato-Oncology, Edmond and Lilly Safra Children's Hospital, Sheba Medical Center, Tel Hashomer 2 Sheba Road, 52621, Ramat Gan, Israel
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, USA
- Instituto Gonçalo MonizFundação Oswaldo Cruz, Salvador, Bahia, Brazil
| | - Gregg S Gonsalves
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, USA
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, School of Medicine and Surgery, Tor Vergata University of Rome, Via Montpellier 1, 00133, Rome, Italy.
- IRCCS Neuromed, 86077, Pozzilli, IS, Italy.
- Department of Pharmacology, School of Medicine, University of Nevada, 89557, Reno, NV, USA.
| | - Juergen K V Reichardt
- Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield, QLD, 4878, Australia
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10
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Ren S, Chen H, Yuan L, Yang X, Afera TB, Rehman ZU, Wang H, Wang X, Ma C, Lin Y, Qiu X, Yin X, Sun Y. Phylogenetic and pathogenic characterization of lumpy skin disease virus circulating in China. Virology 2023; 585:127-138. [PMID: 37336054 DOI: 10.1016/j.virol.2023.06.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/02/2023] [Accepted: 06/08/2023] [Indexed: 06/21/2023]
Abstract
The genomic characterization of emerging pathogens is critical for unraveling their origin and tracking their dissemination. Lumpy skin disease virus (LSDV) is a rapidly emerging pathogen in Asia including China. Although the first Lumpy skin disease (LSD) outbreak was reported in 2019, the origin, transmission, and evolutionary trajectory of LSDV in China have remained obscure. The viral genome of a circulating LSDV strain in China, abbreviated LSDV/FJ/CHA/2021, was sequenced using the next-generation sequencing technique. The morphology and cytoplasmic viral factory of these LSDV isolates were observed using transmission electron microscopy. Subsequently, the genomic characterization of this LSDV isolate was systematically analyzed for the first time using the bioinformatics software. The current study revealed that several mutations in the genome of LSDV isolates circulating in China were identified using single nucleotide polymorphisms (SNPs) analysis, an instrument to evaluate for continuous adaptive evaluation of a virus. Furthermore, phylogenomic analysis was used to identify the lineage using the whole genome sequences of 44 LSDV isolates. The result revealed that the isolates from China were closely similar to that of the LSDV isolates from Vietnam, which are divided into a monophyletic lineage sub-group I. The SNPs and Simplot analysis indicate no significant occurrence of the recombinant event on the genome of LSDV isolates in China. Notably, the live virus challenge experiment demonstrated that the pathogenic characterization of this LSDV isolate belongs to a virulent strain. Collectively, we gain the first insight into the evolutionary trajectory, spatiotemporal transmission, and pathogenic characterization of circulating LSDV in China. This study provides a unique reference for risk assessment, guiding diagnostics, and prevention in epizootic and non-epizootic areas.
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Affiliation(s)
- Shanhui Ren
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730030, PR China
| | - Haotai Chen
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730030, PR China.
| | - Lvfeng Yuan
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730030, PR China
| | - Xue Yang
- Laboratory of Veterinary Microbiology, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Tadele Berihun Afera
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730030, PR China
| | - Zaib Ur Rehman
- Department of Poultry Science, Faculty of Veterinary and Animal Sciences, PMAS-Arid Agriculture University, Rawalpindi, 46300, Pakistan
| | - Huibao Wang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730030, PR China
| | - Xiangwei Wang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730030, PR China
| | - Chunling Ma
- Laboratory of Veterinary Microbiology, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Yuguang Lin
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730030, PR China; Laboratory of Veterinary Microbiology, College of Animal Science and Technology, Tarim University, Alar, 843300, PR China
| | - Xusheng Qiu
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute. Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China
| | - Xiangping Yin
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730030, PR China
| | - Yuefeng Sun
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730030, PR China.
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11
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Ren H, Ling Y, Cao R, Wang Z, Li Y, Huang T. Early warning of emerging infectious diseases based on multimodal data. BIOSAFETY AND HEALTH 2023; 5:S2590-0536(23)00074-5. [PMID: 37362865 PMCID: PMC10245235 DOI: 10.1016/j.bsheal.2023.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/18/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has dramatically increased the awareness of emerging infectious diseases. The advancement of multiomics analysis technology has resulted in the development of several databases containing virus information. Several scientists have integrated existing data on viruses to construct phylogenetic trees and predict virus mutation and transmission in different ways, providing prospective technical support for epidemic prevention and control. This review summarized the databases of known emerging infectious viruses and techniques focusing on virus variant forecasting and early warning. It focuses on the multi-dimensional information integration and database construction of emerging infectious viruses, virus mutation spectrum construction and variant forecast model, analysis of the affinity between mutation antigen and the receptor, propagation model of virus dynamic evolution, and monitoring and early warning for variants. As people have suffered from COVID-19 and repeated flu outbreaks, we focused on the research results of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses. This review comprehensively viewed the latest virus research and provided a reference for future virus prevention and control research.
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Affiliation(s)
- Haotian Ren
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yunchao Ling
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ruifang Cao
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhen Wang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yixue Li
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024 China
- Guangzhou Laboratory, Guangzhou 510005, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200433, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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12
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Rochman ND. In viral games, refs go to the replay. EMBO Rep 2023; 24:e56992. [PMID: 36876587 PMCID: PMC10074127 DOI: 10.15252/embr.202356992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 03/07/2023] Open
Abstract
After more than 2 years of intensive investigation, the direct ancestors of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remain unidentified. Molecular epidemiology strongly supports a timeline marked by multiple, independent zoonoses in late 2019 (Pekar et al, 2022) solidifying the consensus hypothesis that close relatives of SARS-CoV-2 with high zoonotic potential were naturally circulating prior to the start of the pandemic (Andersen et al, 2020). Understanding where and when these ancestors acquired the genomic features that resulted in a virus with epidemic potential could enable the identification and mitigation of future pandemic viruses, even before the first human infection.
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Affiliation(s)
- Nash D Rochman
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
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13
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It takes a village to build a virus. Proc Natl Acad Sci U S A 2023; 120:e2219052120. [PMID: 36701364 PMCID: PMC9945952 DOI: 10.1073/pnas.2219052120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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14
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Junk mail: Viral envelopes promote zoonoses. Proc Natl Acad Sci U S A 2023; 120:e2219962120. [PMID: 36623201 PMCID: PMC9933117 DOI: 10.1073/pnas.2219962120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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15
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Enveloped viruses show increased propensity to cross-species transmission and zoonosis. Proc Natl Acad Sci U S A 2022; 119:e2215600119. [PMID: 36472956 PMCID: PMC9897429 DOI: 10.1073/pnas.2215600119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The transmission of viruses between different host species is a major source of emerging diseases and is of particular concern in the case of zoonotic transmission from mammals to humans. Several zoonosis risk factors have been identified, but it is currently unclear which viral traits primarily determine this process as previous work has focused on a few hundred viruses that are not representative of actual viral diversity. Here, we investigate fundamental virological traits that influence cross-species transmissibility and zoonotic propensity by interrogating a database of over 12,000 mammalian virus-host associations. Our analysis reveals that enveloped viruses tend to infect more host species and are more likely to be zoonotic than nonenveloped viruses, while other viral traits such as genome composition, structure, size, or the viral replication compartment play a less obvious role. This contrasts with the previous notion that viral envelopes did not significantly impact or even reduce zoonotic risk and should help better prioritize outbreak prevention efforts. We suggest several mechanisms by which viral envelopes could promote cross-species transmissibility, including structural flexibility of receptor-binding proteins and evasion of viral entry barriers.
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16
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Overduin M, Tran A, Eekels DM, Overduin F, Kervin TA. Transmembrane Membrane Readers form a Novel Class of Proteins That Include Peripheral Phosphoinositide Recognition Domains and Viral Spikes. MEMBRANES 2022; 12:1161. [PMID: 36422153 PMCID: PMC9692390 DOI: 10.3390/membranes12111161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Membrane proteins are broadly classified as transmembrane (TM) or peripheral, with functions that pertain to only a single bilayer at a given time. Here, we explicate a class of proteins that contain both transmembrane and peripheral domains, which we dub transmembrane membrane readers (TMMRs). Their transmembrane and peripheral elements anchor them to one bilayer and reversibly attach them to another section of bilayer, respectively, positioning them to tether and fuse membranes while recognizing signals such as phosphoinositides (PIs) and modifying lipid chemistries in proximity to their transmembrane domains. Here, we analyze full-length models from AlphaFold2 and Rosetta, as well as structures from nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, using the Membrane Optimal Docking Area (MODA) program to map their membrane-binding surfaces. Eukaryotic TMMRs include phospholipid-binding C1, C2, CRAL-TRIO, FYVE, GRAM, GTPase, MATH, PDZ, PH, PX, SMP, StART and WD domains within proteins including protrudin, sorting nexins and synaptotagmins. The spike proteins of SARS-CoV-2 as well as other viruses are also TMMRs, seeing as they are anchored into the viral membrane while mediating fusion with host cell membranes. As such, TMMRs have key roles in cell biology and membrane trafficking, and include drug targets for diseases such as COVID-19.
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Affiliation(s)
- Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Anh Tran
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | | | - Finn Overduin
- Institute of Nutritional Science, University of Potsdam, 14476 Potsdam, Germany
| | - Troy A. Kervin
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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17
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Colson P, Delerce J, Marion-Paris E, Lagier JC, Levasseur A, Fournier PE, La Scola B, Raoult D. A 21L/BA.2-21K/BA.1 "MixOmicron" SARS-CoV-2 hybrid undetected by qPCR that screen for variant in routine diagnosis. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 105:105360. [PMID: 36070806 PMCID: PMC9444252 DOI: 10.1016/j.meegid.2022.105360] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 01/05/2023]
Abstract
Among the multiple SARS-CoV-2 variants identified since summer 2020, several have co-circulated, creating opportunities for coinfections and potentially genetic recombinations that are common in coronaviruses. Viral recombinants are indeed beginning to be reported more frequently. Here, we describe a new SARS-CoV-2 recombinant genome that is mostly that of a Omicron 21L/BA.2 variant but with a 3' tip originating from a Omicron 21K/BA.1 variant. Two such genomes were obtained in our institute from adults sampled in February 2022 in university hospitals of Marseille, southern France, by next-generation sequencing carried out with the Illumina or Nanopore technologies. The recombination site was located between nucleotides 26,858-27,382. In the two genomic assemblies, mean sequencing depth at mutation-harboring positions was 271 and 1362 reads and mean prevalence of the majoritary nucleotide was 99.3 ± 2.2% and 98.8 ± 1.6%, respectively. Phylogeny generated trees with slightly different topologies according to whether genomes analyzed were depleted or not of the 3' tip. This 3' terminal end brought in the Omicron 21L/BA.2 genome a short transposable element of 41 nucleotides named S2m that is present in most SARS-CoV-2 except a few variants among which the Omicron 21L/BA.2 variant and may be involved in virulence. Importantly, this recombinant is not detected by currently used qPCR that screen for variants in routine diagnosis. The present observation emphasizes the need to survey closely the genetic pathways of SARS-CoV-2 variability by whole genome sequencing, and it could contribute to gain a better understanding of factors that lead to observed differences between epidemic potentials of the different variants.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005 Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France.
| | - Jeremy Delerce
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Elise Marion-Paris
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Hôpital Timone, Service de médecine du travail, 264 rue Saint-Pierre, 13005 Marseille, France
| | - Jean-Christophe Lagier
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005 Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005 Marseille, France
| | - Pierre-Edouard Fournier
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), 27 boulevard Jean Moulin, 13005 Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005 Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005 Marseille, France
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18
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Rochman ND, Wolf YI, Koonin EV. Molecular adaptations during viral epidemics. EMBO Rep 2022; 23:e55393. [PMID: 35848484 PMCID: PMC9346483 DOI: 10.15252/embr.202255393] [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: 05/12/2022] [Revised: 06/18/2022] [Accepted: 06/27/2022] [Indexed: 07/20/2023] Open
Abstract
In 1977, the world witnessed both the eradication of smallpox and the beginning of the modern age of genomics. Over the following half-century, 7 epidemic viruses of international concern galvanized virologists across the globe and led to increasingly extensive virus genome sequencing. These sequencing efforts exerted over periods of rapid adaptation of viruses to new hosts, in particular, humans provide insight into the molecular mechanisms underpinning virus evolution. Investment in virus genome sequencing was dramatically increased by the unprecedented support for phylogenomic analyses during the COVID-19 pandemic. In this review, we attempt to piece together comprehensive molecular histories of the adaptation of variola virus, HIV-1 M, SARS, H1N1-SIV, MERS, Ebola, Zika, and SARS-CoV-2 to the human host. Disruption of genes involved in virus-host interaction in animal hosts, recombination including genome segment reassortment, and adaptive mutations leading to amino acid replacements in virus proteins involved in host receptor binding and membrane fusion are identified as the key factors in the evolution of epidemic viruses.
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Affiliation(s)
- Nash D Rochman
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
| | - Yuri I Wolf
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
| | - Eugene V Koonin
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
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