Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

Nature, Journal Year: 2022, Volume and Issue: 603(7902), P. 679 - 686

Published: Jan. 7, 2022

Abstract The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. first was associated with a mix of lineages, while the second and third waves were driven Beta (B.1.351) Delta (B.1.617.2) variants, respectively 1–3 . In November 2021, genomic surveillance teams South Botswana detected new variant rapid resurgence infections Gauteng province, Africa. Within days genome being uploaded, it designated concern (Omicron, B.1.1.529) World Health Organization and, within weeks, had identified 87 countries. Omicron is exceptional for carrying over 30 mutations spike glycoprotein, which are predicted to influence antibody neutralization function 4 Here we describe profile early transmission dynamics Omicron, highlighting spread regions high levels population immunity.

Language: Английский

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SARS-CoV-2 variant biology: immune escape, transmission and fitness

Nature Reviews Microbiology, Journal Year: 2023, Volume and Issue: unknown

Published: Jan. 18, 2023

In late 2020, after circulating for almost a year in the human population, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exhibited major step change its adaptation to humans. These highly mutated forms of SARS-CoV-2 had enhanced rates transmission relative previous variants and were termed 'variants concern' (VOCs). Designated Alpha, Beta, Gamma, Delta Omicron, VOCs emerged independently from one another, turn each rapidly became dominant, regionally or globally, outcompeting variants. The success VOC previously dominant variant was enabled by altered intrinsic functional properties virus and, various degrees, changes antigenicity conferring ability evade primed immune response. increased fitness associated with is result complex interplay biology context changing immunity due both vaccination prior infection. this Review, we summarize literature on transmissibility variants, role mutations at furin spike cleavage site non-spike proteins, potential importance recombination success, evolution T cells, innate population immunity. shows complicated relationship among antigenicity, virulence, which has unpredictable implications future trajectory disease burden COVID-19.

Language: Английский

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SARS-CoV-2 Omicron variant replication in human bronchus and lung ex vivo

Nature, Journal Year: 2022, Volume and Issue: 603(7902), P. 715 - 720

Published: Feb. 1, 2022

Language: Английский

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Probable Transmission of SARS-CoV-2 Omicron Variant in Quarantine Hotel, Hong Kong, China, November 2021

Emerging infectious diseases, Journal Year: 2021, Volume and Issue: 28(2), P. 460 - 462

Published: Dec. 3, 2021

We report detection of severe acute respiratory syndrome coronavirus 2 Omicron variant (B.1.1.529) in an asymptomatic, fully vaccinated traveler a quarantine hotel Hong Kong, China. The was also detected staying room across the corridor from index patient, suggesting transmission despite strict precautions.

Language: Английский

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The outbreak of SARS‐CoV‐2 Omicron lineages, immune escape, and vaccine effectivity

Journal of Medical Virology, Journal Year: 2022, Volume and Issue: 95(1)

Published: Sept. 13, 2022

As of November 2021, several SARS-CoV-2 variants appeared and became dominant epidemic strains in many countries, including five concern (VOCs) Alpha, Beta, Gamma, Delta, Omicron defined by the World Health Organization during COVID-19 pandemic. August 2022, is classified into main lineages, BA.1, BA.2, BA.3, BA.4, BA.5 some sublineages (BA.1.1, BA.2.12.1, BA.2.11, BA.2.75, BA.4.6) (https://www.gisaid.org/). Compared to previous VOCs (Alpha, Delta), all lineages have most highly mutations spike protein, with 50 accumulated throughout genome. Early data indicated that BA.2 sublineage had higher infectivity more immune escape than early wild-type (WT) strain, VOCs, BA.1. Recently, global surveillance suggest a transmissibility BA.4/BA.5 BA.1.1 becoming strain countries globally.

Language: Английский

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Animal models in SARS-CoV-2 research

Nature Methods, Journal Year: 2022, Volume and Issue: 19(4), P. 392 - 394

Published: April 1, 2022

Language: Английский

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Emerging evidence on Omicron (B.1.1.529) SARS‐CoV‐2 variant

Journal of Medical Virology, Journal Year: 2022, Volume and Issue: 94(5), P. 1876 - 1885

Published: Jan. 27, 2022

COVID's Omicron variant has sparked a slew of concerns across the globe. This review aims to provide brief overview what we know about right now. The new been discovered in 149 countries all six World Health Organization (WHO) regions since its discovery South Africa on November 24, 2021 and became dominant country less than 3 weeks. WHO warned that B.1.1.529 is spreading at an unprecedented rate, urged prepare for worst. Over course this time, researchers from around world have uncovered wealth information virus's epidemiology biological properties. Case numbers are increasing exponentially hard-hit areas such as Africa, United Kingdom, USA (overtaking delta variant), implying highly transmissible. Initial research provided some insights into efficacy vaccines against whether it produces major illness, however, much remains unknown, additional work needed investigate initial reports represent real-world situations.

Language: Английский

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Replication of SARS-CoV-2 Omicron BA.2 variant in ex vivo cultures of the human upper and lower respiratory tract

EBioMedicine, Journal Year: 2022, Volume and Issue: 83, P. 104232 - 104232

Published: Aug. 18, 2022

Language: Английский

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Phase separation by the SARS-CoV-2 nucleocapsid protein: Consensus and open questions

Journal of Biological Chemistry, Journal Year: 2022, Volume and Issue: 298(3), P. 101677 - 101677

Published: Feb. 4, 2022

In response to the recent SARS-CoV-2 pandemic, a number of labs across world have reallocated their time and resources better our understanding virus. For some viruses, including SARS-CoV-2, viral proteins can undergo phase separation: biophysical process often related partitioning protein RNA into membraneless organelles in vivo. this review, we discuss emerging observations separation by nucleocapsid (N) protein—an essential required for replication—and possible vivo functions that been proposed N-protein separation, replication, genomic packaging, modulation host-cell infection. Additionally, since relatively large studies examining published short span time, take advantage situation compare results from similar experiments studies. Our evaluation highlights potential strengths pitfalls drawing conclusions single set experiments, as well value publishing overlapping scientific performed simultaneously multiple labs. virus responsible COVID-19 ongoing has exacted an enormous toll on human health, with >5.6 million deaths >350 infections currently attributed (according World Health Organization data, https://covid19.who.int/, accessed 1/26/22). The pandemic had already led estimated $16 trillion global economic costs October 2020 (1Cutler D.M. Summers L.H. virus.JAMA. 2020; 324: 1495-1496Google Scholar) disrupted nearly every sector, science. Over past year half, extraordinary progress made improving novel Emerging experimental implicate critical factor mediating (gRNA) Intriguingly, N ability (PS), which is now considered pervasive phenomenon organizing broad diversity biological processes cells. models, results, PS protein. given remarkable publications topic within ∼ 1 year, leverage unusual evaluate how work, parallel independent groups, may shape resulting conclusions. practice, science sequentially: one discovery typically precedes, informs, directs subsequent experimentation. incentive structure science, rewards novelty, promotes sequential model, disincentivizes focused replication validation. One limitation model subtle differences design sometimes significant impact thus influence direction experiments. However, publication was punctuated pandemic. Many historically little or no prior experience virology applied respective areas expertise questions SARS-CoV-2. This abrupt reallocation same study many organically created question its own: what happens when perform publish closely parallel? Here, reporting examine question. prototypical function coronaviral condense organize gRNA nascent virions (2Chang C. Hou M.-H. Chang C.-F. Hsiao C.-D. Huang T.-H. SARS coronavirus - forms functions.Antiviral Res. 2014; 103: 39-50Google Scholar). Virion formation occurs via accumulation structural [the spike (S), envelope (E), membrane (M), proteins] at ER-Golgi intermediate compartment (ERGIC) membrane. Multiple suggest strand dense, locally ordered ribonucleoprotein (RNP) regions consisting predominantly associated (3Klein S. Cortese M. Winter S.L. Wachsmuth-Melm Neufeldt C.J. Cerikan B. Stanifer M.L. Boulant Bartenschlager R. Chlanda P. characterized situ cryo-electron tomography.Nat. Commun. 11: 5885Google Scholar, 4Yao H. Song Y. Chen Wu N. Xu J. Sun Zhang Weng T. Z. Cheng L. Shi D. Lu X. Lei Crispin et al.Molecular architecture virus.Cell. 183: 730-738.e13Google 5Cao Cai Xiao Rao Hu Yang Xing Wang Li Zhou Xue genome inside virion.Nat. 2021; 12: 3917Google Locally RNPs be further organized more complex arrangements clustering particular stoichiometries geometries Scholar), although other evidence models SARS-CoV linear, helical RNP arrangement 6Filho H.V.R. Jara G.E. Batista F.A.H. Schleder G.R. Tonoli C.C. Soprano A.S. Guimarães Borges A.C. Cassago A. Bajgelman M.C. Marques R.E. Trivella D.B.B. Franchini K.G. Figueira A.C.M. Benedetti C.E. al.Structural dynamics induced binding.bioRxiv. ([preprint])https://doi.org/10.1101/2021.08.27.457964Google These preferentially accumulate curved membranes indicating either association aids curvature during virion formation, are preferred recruitment surface RNPs. also interacts luminal domain (i.e., interior virions) M protein, mechanism N-containing ERGIC (7Lu Ye Q. Singh Cao Diedrich J.K. Yates J.R. Villa E. Cleveland D.W. Corbett K.D. phosphoprotein mutually exclusive condensates membrane-associated protein.Nat. 502Google Some suggests both interact E (8Tseng Y.-T. S.-M. K.-J. C.-T. palmitoylation nucleocapid not promoting virus-like particle production.J. Biomed. Sci. 21: 34Google 9Li Guo Tian Liu Qu Yin Zhu Peng al.Virus-host interactome proteomic survey reveal virulence factors influencing pathogenesis.Med. (N. Y.). 2: 99-112.e7Google While precise detail regarding interactions individual molecules intact still forthcoming, clearly plays central role compaction organization virions. involves two distinct yet coexisting phases well-mixed solution: dense high concentration dilute low (10Banani S.F. Lee H.O. Hyman A.A. Rosen M.K. Biomolecular condensates: Organizers cellular biochemistry.Nat. Rev. Mol. Cell Biol. 2017; 18: 285-298Google Subsequent initial PS, additional transitions change material properties (11Patel Jawerth Maharana Jahnel Hein M.Y. Stoynov Mahamid Saha Franzmann T.M. Pozniakovski Poser I. Maghelli Royer L.A. Weigert al.A liquid-to-solid transition ALS FUS accelerated disease mutation.Cell. 2015; 162: 1066-1077Google 12Molliex Temirov Coughlin Kanagaraj A.P. Kim H.J. Mittag Taylor J.P. Phase complexity domains stress granule assembly drives pathological fibrillization.Cell. 163: 123-133Google Consequently, exhibit consistent liquids, gels, solids (13Boeynaems Alberti Fawzi N.L. Polymenidou Rousseau F. Schymkowitz Shorter Wolozin Van Den Bosch Tompa Fuxreiter Protein A new cell biology.Trends 2018; 28: 420-435Google these influenced sequence, concentration, presence concentrations molecules, physical chemical environment. key features “multivalency,” describes binding sites partner molecules. occur single-component multicomponent systems (14Dignon G.L. Best R.B. Mittal From molecular driving forces macroscopic properties.Annu. Phys. Chem. 71: 53-75Google 15Ruff K.M. Dar Pappu R.V. Polyphasic linkage ligand regulation biomolecular condensates.Biophys. 2021302Google system, driven homotypic between identical biopolymers), whereas co-PS system heterotypic different biopolymers) combination interactions. type multivalent observe certain appear common among known separate. example, separating contain RNA-binding domains, intrinsically disordered (IDRs), oligomerization low-complexity domains. gained attention biology due connection “biomolecular condensates” 13Boeynaems 16Hyman Weber C.A. Jülicher Liquid-liquid biology.Annu. Dev. 30: 39-58Google enriched nucleic acids. Much like observed vitro, consist network (often acids, proteins, biopolymers). types described, (but limited to) granules, P-bodies, nucleoli, nuclear speckles, germ Cajal bodies Each condensate sets constituent properties, functions, stability, regulation. Regardless differences, condensation represents elegant solution concentrating groups regulatable sensitive fashion. Given prevalence, diversity, importance eukaryotes, it perhaps surprise viruses able manipulate endogenous trigger entirely host cells (17Gaete-Argel Márquez C.L. Barriga G.P. Soto-Rifo Valiente-Echeverría Strategies success. Viral organelles.Front. Cell. Infect. Microbiol. 2019; 9: 336Google 18Etibor T.A. Yamauchi Amorim M.J. Liquid lifecycles: Review perspectives.Viruses. 13: 366Google Shortly after emergence would behavior might mediate RNA–protein packaging virions, modulate (namely, granules) direct interaction (19Cascarina S.M. Ross E.D. condensates.FASEB 34: 9832-9842Google ensuing months, various aspects modulation, innate immune pathways, kinases, were formally 20Zhao Yu L.-M. J.-Q. W. Xia Han Q.-Y. W.-H. A.-L. al.GCG inhibits disrupting liquid 2114Google 21Iserman Roden Boerneke M.A. Sealfon R.S.G. McLaughlin G.A. Jungreis Fritch E.J. Y.J. Ekena Weidmann Theesfeld Kellis Troyanskaya O.G. Baric R.S. Sheahan T.P. al.Genomic elements drive nucleocapsid.Mol. 80: 1078-1091.e6Google 22Cubuk Alston J.J. Incicco Stuchell-Brereton M.D. Ward Zimmerman M.I. Vithani Griffith Wagoner J.A. Bowman Hall K.B. Soranno Holehouse dynamic, disordered, separates RNA.Nat. 1936Google 23Dang ATP biphasically modulates LLPS specifically binds domain.Biochem. Biophys. 541: 50-55Google 24Zhao Nguyen Adão R.C. Valkov Patterson G.H. Piszczek G. Schuck Energetic co-assemblies acids.iScience. 24: 102523Google 25Wang Dai Qin Pan Chu Lou Targeting liquid–liquid antiviral immunity elevating MAVS activity.Nat. 23: 718-732Google 26Huang Ju Ding Jia Molecular determinants G3BP1/2 protein.Cell Discov. 7: 69Google 27Prakash Somasekharan Gleave immunoregulators granules form droplets.FEBS Lett. 595: 2872-2896Google 28Jack Ferro L.S. Trnka Wehri Nadgir Nguyenla Fox Costa K. Stanley Schaletzky Yildiz RNA.PLoS 19e3001425Google 29Savastano Ibáñez de Opakua Rankovic Zweckstetter Nucleocapsid RNA-rich polymerase-containing condensates.Nat. 6041Google 30Carlson C.R. Asfaha J.B. Ghent C.M. Howard Hartooni Safari Frankel A.D. Morgan D.O. Phosphoregulation basis dual functions.Mol. 1092-1103.e4Google 31Luo Zhao Ma Jin He Zou Liang Chi al.SARS-CoV-2 G3BPs disassemble facilitate production.Sci. Bull. 66: 1194-1204Google 32Perdikari Murthy Ryan V.H. Watters Naik M.T. phase-separates hnRNPs.EMBO 39e106478Google 33Wang undergoes through N-terminal region.Cell 5Google 34Wu Zhuang Xie Cui RNA-induced facilitates NF-κB hyper-activation inflammation.Signal Transduct. Target. Ther. 6: 167Google 35Chen P.H. Liquid–liquid RNA.Cell 1143-1145Google 36Zhao Ge Yuan Xiong Feng Shu Lang al.Understanding characteristics provides therapeutic opportunity against SARS-CoV-2.Protein 734-740Google Figure affecting vitro vivo, each discussed sections. purported and, broadly, learned “consensus” view timeframe. We note while done best faithfully interpret available all present rigorous quantification methods differed studies; therefore, based least degree subjective interpretation. containing prion-like (37Fomicheva prions granules: Defining compositional promote assemblies.Int. 22: 1251Google 38March Z.M. King O.D. Prion-like epigenetic regulators, scaffolds subcellular organization, drivers neurodegenerative disease.Brain 2016; 1647: 9-18Google 39Harrison A.F. health disease.Biochem. 474: 1417-1438Google itself capable undergoing (40Van Treeck Protter D.S.W. Matheny Khong Link C.D. Parker self-assembly contributes defining transcriptome.Proc. Natl. Acad. U. 115: 2734-2739Google induce specific lower (41Lin maturation phase-separated droplets proteins.Mol. 60: 208-219Google regulate variety ways [reviewed (42Roden Gladfelter contributions 183-195Google Scholar)]. contains structured (43Zhou Zeng von Brunn Structural characterization C-terminal protein.Mol. 1: 2Google 44Yang Kang insight reveals recognition transcriptional regulatory sequences.Front. 8: 624765Google 45Peng Du Dorje Qi Luo Gao G.F. Structures perspectives drug design.EMBO 39e105938Google 46Kang Hong Yan Shan Crystal unique targeting sites.Acta Pharm. Sin. 10: 1228-1238Google 47Wu Qavi A.J. Hachim Kavian Cole A.R. Moyle A.B. Wagner N.D. Sweeney-Gibbons Rohrs H.W. Gross Peiris J.S.M. Basler C.F. Farnsworth C.W. Valkenburg S.A. Amarasinghe G.K. al.Characterization functional consequences domain.iScience. 102681Google flanking IDRs enhance (44Yang alone exhibited weak undetectable majority almost universally evaluated depth (Fig. 1Ai). RNAs varying lengths sequences degrees, suggesting somewhat nonspecific (though N+RNA greater sequence specificity, later section). tested wide range concentrations, exceedingly amounts tended inhibit re-entrant imbalance Electrostatic consistently implicated regulating RNA-dependent 1Aii). salt salts used (48Alberti Considerations challenges studying liquid-liquid condensates.Cell. 176: 419-434Google generally presumed reflect electrostatic PS. Lower enhanced (20Zhao throu

Language: Английский

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Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

Nature, Journal Year: 2022, Volume and Issue: unknown

Published: Jan. 7, 2022

The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. first was associated with a mix of lineages, while the second and third waves were driven Beta (B.1.351) Delta (B.1.617.2) variants, respectively1–3. In November 2021, genomic surveillance teams South Botswana detected new variant rapid resurgence infections Gauteng province, Africa. Within days genome being uploaded, it designated concern (Omicron, B.1.1.529) World Health Organization and, within weeks, had identified 87 countries. Omicron is exceptional for carrying over 30 mutations spike glycoprotein, which are predicted to influence antibody neutralization function4. Here we describe profile early transmission dynamics Omicron, highlighting spread regions high levels population immunity. strain SARS-CoV-2.

Language: Английский

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