Evolutionary analysis of SARS-CoV-2: how mutation of Non-Structural Protein 6 (NSP6) could affect viral autophagy.
Domenico Benvenuto,Silvia Angeletti,Marta Giovanetti,Martina Bianchi,Stefano Pascarella,Roberto Cauda,Massimo Ciccozzi,Antonio Cassone +7 more
TLDR
Genome follow-up of SARS-CoV-2 spread is urgently needed in order to identify mutations that could significantly modify virus pathogenicity.About:
This article is published in Journal of Infection.The article was published on 2020-04-10 and is currently open access. It has received 212 citations till now. The article focuses on the topics: Mutation & Genome.read more
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JPred4: A protein secondary structure prediction server
TL;DR: The JPred4 web server has been re-implemented in the Bootstrap framework and JavaScript to improve its design, usability and accessibility from mobile devices and the help-pages have been updated and tool-tips added as well as step-by-step tutorials.
Journal ArticleDOI
The emergence and epidemic characteristics of the highly mutated SARS‐CoV‐2 Omicron variant
TL;DR: The current review article aims to analyze and summarize information data about the biological characteristics of amino acid mutations, the epidemic characteristics, immune escape, and vaccine reactivity of the Omicron variant, hoping to provide a scientific reference for monitoring, prevention, and vaccines development strategies for the OMicron variant.
Journal ArticleDOI
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway
Brian J. Willett,Joe Grove,Oscar A. MacLean,Craig Wilkie,Giuditta De Lorenzo,Wilhelm Furnon,Diego Cantoni,S. Scott,Nicola S Logan,Shirin Ashraf,M. Manali,Agnieszka M. Szemiel,Vanessa M. Cowton,Elen Vink,Chris Davis,Patawee Asamaphan,Richard J. Orton,P Holland,Vanessa Silva,David J Pascall,Kathryn Puxty,Sharif Shaaban Muhammad Shaaban,Matthew T. G. Holden,Rute Maria Pinto,Kate Templeton,Pablo R. Murcia,Arvind H. Patel,Paul Klenerman,Susanna Dunachie,Eleanor Barnes,Anthony Brown,S Adele,Barbara Kronsteiner,Sam M. Murray,P. Abraham,Alexandra Deeks,M A Ansari,Lance Turtle,Shona C Moore,James Austin,Alex G. Richter,Christopher J A Duncan,Rebecca Payne,Amy Ehrlich Ash,C. J. Koshy,Beatrix Kele,Teresa Cutino-Moguel,Derek Fairley,James McKenna,Tanya Curran,Helen Adams,Christophe Fraser,David Bonsall,Helen R. Fryer,Katrina A. Lythgoe,Laura Hayden Thomson,Tanya Golubchik,Abigail Murray,D. Singleton,Shaun M. Beckwith,A Mantzouratou,Magdalena Barrow,Sarah L. Buchan,Nicola Reynolds,Ben Warne,Joshua Maksimovic,Karla Spellman,Kathryn Mccluggage,M. John,Robert H. Beer,Safiah Afifi,Sian Natasha Morgan,Andrew L. Mack,Angela Marchbank,Anna Price,A.C. Morriss,Catherine Bresner,Christine Kitchen,I. Merrick,Joel Southgate,Martyn F Guest,Owen Bowden Jones,Robert F. Munn,Thomas R. Connor,Tom Whalley,T. Race Workman,William Oliver Fuller,Amita Patel,Bindi Patel,G. Nebbia,Jonathan D. Edgeworth,Luke B Snell,Rahul Batra,Themoula Charalampous,Angela Helen Beckett,Ekaterina Shelest,Samuel Robson,Anthony Underwood,Benjamin Taylor,Corin Yeats,David M. Aanensen,Khalil Abudahab,Mirko Menegazzo,Amelia Joseph,Gemma Clark,Hannah C. Howson-Wells,Louise Berry,Manjinder Khakh,Michelle Lister,T. Boswell,Vicki M. Fleming,Christopher W Holmes,Claire McMurray,Jessica R. Shaw,Julian W. Tang,Karlie Fallon,Minaxshi Odedra,Nicholas J. Willford,Paul W Bird,Thomas Helmer,L.A. Williams,Nicole R. Sheriff,Sharon Campbell,Veena Raviprakash,Vickie L. Blakey,Christopher I. Moore,Fei Sang,Johnny Debebe,Matthew Carlile,Matthew Loose,Nadine Holmes,Victoria Wright,M. Torok,William L Hamilton,Alessandro M Carabelli,Andrew Jermy,Beth Blane,Carol Churcher,Catherine Ludden,Dinesh Aggarwal,Elaine J. Westwick,Ellen Brigid Brooks,Georgina M. McManus,Katerina Galai,Ken R. Smith,Kim Smith,MacGregor Cox,Mireille Fragakis,Patrick Maxwell,Sarah Judges,Sharon J. Peacock,Theresa Feltwell,A. K. Kenyon,Sahar Eldirdiri,Thomas Davis,Joshua F. Taylor,NgeeKeong Tan,Alexander E. Zarebski,Bernardo Gutierrez,Jayna Raghwani,Louis du Plessis,Moritz U. G. Kraemer,Oliver G. Pybus,Sarah François,S. W. Attwood,Tetyana I. Vasylyeva,Aminu S Jahun,Ian Goodfellow,Iliana Georgana,Malte L Pinckert,Myra Hosmillo,Rhys E. Izuagbe,Yasmin Chaudhry,Felicity Ryan,Hannah Louise Lowe,Samuel Rajan Moses,Luke Bedford,James S Cargill,Warwick S. Hughes,J. Moore,Susanne Stonehouse,Divya Shah,Jack Lee,Julianne R Brown,Kathryn A. Harris,Laura Atkinson,Nathaniel Storey,Moira J. Spyer,Flavia Flaviani,Adela Alcolea-Medina,J. Sehmi,John Ramble,Natasha Ohemeng-Kumi,P. Smith,B. Bertolusso,Claire P Thomas,Gabrielle Vernet,Jessica Lynch,Nathan Moore,Nicholas Cortes,Rebecca Williams,Stephen P. Kidd,L. J. Levett,Monika Pusok,Paul Grant,Stuart Kirk,W. J. Chatterton,Li Xu-McCrae,Darren L. Smith,Gregor Young,Matthew Bashton,Katie Kitchman,Kavitha Gajee,K. Eastick,Patrick J. Lillie,Phillipa Burns,William G. Everson,Alison Cox,Alison Holmes,Frances Bolt,James R. Price,Marcus Pond,Paul Randell,Pinglawathee Madona,Siddharth Mookerjee,Erik M. Volz,Lily Geidelberg,Manon Ragonnet-Cronin,Olivia Boyd,Robert Johnson,Cassie F Pope,Adam A. Witney,Irene M. Monahan,Ken Laing,Katherine Smollett,Alan McNally,Joanne Stockton,Joshua Quick,Nicholas J. Loman,Radoslaw Poplawski,Samuel M. Nicholls,Will P. M. Rowe,Anibolina Castigador,Emily Macnaughton,Kate El Bouzidi,Malur Sudhanva,Temi Lampejo,Rocio Martinez Nunez,Cathy Breen,Graciela Sluga,Karen T. Withell,Nicholas W Machin,Ryan George,Shazaad Ahmad,David Pritchard,D. Binns,Nick Wong,Victoria L. James,Cheryl Williams,Christopher J. R. Illingworth,Christopher Jackson,Daniela De Angelis,Afrida Mukaddas,Alice Broos,Ana da Silva Filipe,Daniel Mair,David Robertson,Derek W. Wright,E. Thomson,Igor Starinskij,Ioulia Tsatsani,James Shepherd,Jenna Nichols,Joseph Hughes,Kyriaki Nomikou,Lily Tong,Sreenu B. Vattipally,William T. Harvey,Roy A. Sanderson,S. O’Brien,Steven Rushton,Jon Davis Perkins,Rachel Blacow,Rory Gunson,A. Gallagher,Elizabeth Wastnedge,Martin P McHugh,Rebecca Dewar,Seb Cotton,Lindsay Coupland,R.Suganya and Dr. Shaleesha A. Stanley,Samir Dervisevic,Lewis G. Spurgin,Louise Smith,Clive Graham,D. Padgett,Edward Barton,Garren Scott,Aidan Cross,Mariyam Mirfenderesky,E. Swindells,J Greenaway,Rebecca Denton-Smith,Robyn Turnbull,Giles Idle,Kevin Cole,Amy Louise Hollis,Andrew T. Nelson,C. McCann,Joan H Henderson,M. Crown,Wen Chyin Yew,W Stawski Stanley,Nicholas Duckworth,Phillip Clarke,Sarah Walsh,Tim J. Sloan,Kelly Bicknell,R. L. Impey,Sarah Wyllie,Scott M. Elliott,Sharon Glaysher,Declan Bradley,Nicholas Killough,Tim W. Wyatt,Andrew Bosworth,Barry Vipond,Clare Pearson,Elias Allara,E. E Robinson,Hannah M. Pymont,Husam Osman,Peter C. Muir,Richard Hopes,S. A. Hutchings,Martin D. Curran,Surendra S. Parmar,A Thornton,Angie Lackenby,Chloe Bishop,David F. Bibby,Dave Lee,Eileen Gallagher,Gavin Dabrera,Ian Harrison,Jonathan Hubb,Katherine A. Twohig,Meera Chand,Nicholas Ellaby,Nikos Manesis,R. Myers,Steven Platt,Tamyo Mbisa,Vicki Chalker,Gonzalo Yebra,Stefan Rooke,Alec Birchley,Alexander Adams,A Davies,Amy E. Gaskin,Bree Gatica-Wilcox,Caoimhe McKerr,Catherine Moore,Catryn Williams,Chris Williams,David Heyburn,Elen de Lacy,Ember Hilvers,Fatima Downing,Georgia Pugh,Hannah Jones,Hibo Asad,Jason D. Coombes,Jessica G. Hey,Jessica L. Powell,Joanne Watkins,John Evans,Laia Fina,Laura Gifford,L Gilbert,Lee H. Graham,Malorie Perry,Mari Morgan,Matthew Bull,Nicole Pacchiarini,Noel Craine,Sally Corden,Sara Kumžiene-Summerhayes,Sara Rey,Sarah Taylor,Simon Cottrell,Sophie Jones,Sue Edwards,Tara Annett,Alexander J. Trotter,Alison E. Mather,Alp Aydin,Andrew J. Page,David J. Baker,Ebenezer Foster-Nyarko,Gemma L. Kay,Justin O'Grady,Leonardo de Oliveira Martins,Lizzie Meadows,Nabil-Fareed Alikhan,Sophie J Prosolek,Steven J. Rudder,Thanh Le-Viet,Anna Casey,Liz Ratcliffe,Aditi Singh,Arun Mariappan,Chris L. Baxter,Clara Radulescu,David Simpson,Debra Redman Lavin,Fiona Rogan,Julia Miskelly,Marc Fuchs,Miao Tang,Sílvia F. Carvalho,Stephen Bridgett,Timofey Skvortsov,Zoltán Molnár,Newara Ramadan,Bridget A. Knight,Christopher R. Jones,Cressida Auckland,Helen Morcrette,Jennifer Lee Poyner,Dianne Irish-Tavares,Eric Witele,Jennifer Hart,Tabitha Mahungu,Tanzina Haque,Yann Bourgeois,Christopher Fearn,Kate Cook,Katie F. Loveson,Salman Goudarzi,Cariad Evans,David G Partridge,Katie Johnson,Mehmet Yavus,Mohammad Raza,Craig Mower,Paul Baker,Sarah Essex,Stephen Bonner,Leanne Murray,Louisa K. Watson,Steven P. Liggett,Andrew I. Lawton,Ronan A Lyons,Brendan A I Payne,G Eltringham,Jennifer Collins,Sheila Waugh,Shirelle Burton-Fanning,Yusri Taha,Christopher Jeanes,Andrea N. Gomes,Darren Murray,Maimuna Kimuli,D Dobie,Paula Ashfield,Angus I. Best,Benita Percival,Emma Moles-Garcia,F. Ashford,Jeremy Mirza,L. Crawford,Megan Mayhew,Nicola Cumley,Oliver Megram,Dan Frampton,Judith Heaney,Matthew Byott,C. Houlihan,Charlotte A Williams,Eleni Nastouli,Helen Lowe,John A. Hartley,Judith Breuer,Laurentiu Maftei,Leah Ensell,Marius Cotic,Matteo Mondani,Molly Driscoll,N. Bayzid,Rachel Williams,Sunando Sur Roy,Adhyana I K Mahanama,Buddhini Samaraweera,Eleri Wilson-Davies,Emanuela Pelosi,H.C Umpleby,Helen Wheeler,Jacqui Prieto,Kordo Saeed,Matthew Harvey,Sarah Jeremiah,Siona Silviera,Stephen Aplin,T. Sass,BS Macklin,Dorian Crudgington,Liz Sheridan,Benjamin J. Cogger,Cassandra Malone,Florence Munemo,Hannah Huckson,Jonathan Lewis,Lisa J. Easton,Manasa Mutingwende,Michelle J. Erkiert,Mohammed O. Hassan-Ibrahim,N. Chaloner,Olga Podplomyk,Paul Randell,Roberto Nicodemi,Sarah L. Lowdon,Thomas Somassa,Andrew Beggs,Andrew Hesketh,Colin P. Smith,Giselda Bucca,Christopher Ruis,Claire Cormie,Ellen E. Higginson,Jamie Young,Joana Dias,L. Kermack,Mailis Maes,Ravi Gupta,Sally Forrest,Sophia T. Girgis,Rose K Davidson,Áine O'Toole,Andrew Rambaut,Ben Jackson,Carlos Balcazar,Daniel S. Maloney,Emily Scher,J. McCrone,Katherine A. Williamson,Michael D. Gallagher,Nathan C Medd,Rachel M. Colquhoun,Thomas D. Stanton,Thomas C Williams,Verity Hill,Aaron R. Jeffries,Ben Temperton,Christine Sambles,David J. Studholme,Joanna Warwick-Dugdale,Leigh Jackson,Michelle Michelsen,R. Manley,Stephen L. Michell,Alistair C. Darby,Anita Lucaci,Charlotte Nelson,Claudia Wierzbicki,Edith E. Vamos,Hermione J. Webster,Kathryn A. Jackson,Lucille Rainbow,Margaret Lawrence Hughes,Mark Whitehead,Matthew Gemmell,Miren Iturriza-Gomara,Richard Eccles,Richard Gregory,Sam Haldenby,Steve Paterson,Adrienn Angyal,Alexander J Keeley,Benjamin Foulkes,Benjamin B Lindsey,Dennis Wang,Hailey Hornsby,Luke R. Green,Manoj Baliram Pohare,M. Gallis,Matthew Parker,M. Whiteley,Nikki Smith,P. Wolverson,Peijun Zhang,Samantha Hansford,Sharon N. Hsu,S. Louka,Thushan I de Silva,Timothy M. Freeman,Matilde Mori,Emily J. Park,Jack Hill,Jayasree Dey,Jonathan K. Ball,Joseph G. Chappell,Patrick McClure,Timothy Byaruhanga,A Fanaie,Geraldine Yaze,Rachel A. Hilson,Amy Trebes,Angie Green,David Buck,G. Macintyre-Cockett,John A. Todd,Andrew R. Bassett,Andrew Whitwham,Cordelia Langford,Diana Rajan,Dominic P. Kwiatkowski,J. Harrison,Iraad F. Bronner,Jaime M. Tovar-Corona,Jennifier Liddle,Jillian Durham,Katherine L. Bellis,Kevin Lewis,Louise Aigrain,Nicholas Redshaw,Robert L. Davies,Robin J. Moll,Shane A. McCarthy,Stefanie V Lensing,Steven Leonard,Ben Farr,C. Scott,Charlotte M. Beaver,Cristina V. Ariani,Da Weldon,David Jackson,Emma Betteridge,Gerry Tonkin-Hill,Ian Johnston,Inigo Martincorena,James K. Bonfield,Jeffrey C. Barrett,John Sillitoe,J P Keatley,Karen A. Oliver,Keith James,Lesley Shirley,Liam J. Prestwood,Luke Foulser,Marina Gourtovaia,Matthew J. Dorman,Michael A. Quail,Michael Spencer Chapman,Naomi Park,Rich Livett,Roberto Amato,Sally Kay,Scott Goodwin,Scott Thurston,Shavanthi Rajatileka,Sónia Gonçalves,Stephanie Lo,Theo Sanderson,Alasdair MacLean,Emily Goldstein,Lynne Ferguson,Rachael M. Tomb,Jana Catalan,Neil Jones,John Haughney,Massimo Palmarini,Surajit Ray +672 more
TL;DR: In this article , the authors demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273.529.
Posted ContentDOI
The hyper-transmissible SARS-CoV-2 Omicron variant exhibits significant antigenic change, vaccine escape and a switch in cell entry mechanism
Brian J. Willett,Joe Grove,Oscar A. MacLean,Craig Wilkie,Nicola S Logan,Giuditta De Lorenzo,Wilhelm Furnon,Samuel Scott,M. Manali,Agnieszka M. Szemiel,Shirin Ashraf,Elen Vink,William T. Harvey,Chris Davis,Richard J. Orton,Joseph Hughes,P Holland,Vanessa K. A. Silva,David J Pascall,Kathryn Puxty,Ana da Silva Filipe,Gonzalo Yebra,Sharif Shaaban Muhammad Shaaban,Matthew T. G. Holden,Rute Maria Pinto,Rory Gunson,Kate Templeton,Pablo R. Murcia,Arvind H. Patel,John Haughney,David Robertson,Massimo Palmarini,Surajit Ray,E. Thomson +33 more
TL;DR: It is shown that immunity from natural infection (without vaccination) is more protective than two doses of vaccine but inferior to three doses, and fundamental changes in the Omicron entry process in vitro, towards TMPRSS2-independent fusion, representing a major shift in the replication properties of SARS-CoV-2.
Journal ArticleDOI
From SARS and MERS CoVs to SARS-CoV-2: Moving toward more biased codon usage in viral structural and nonstructural genes.
Mahmoud Kandeel,Mahmoud Kandeel,Abdel Azim Ibrahim,Abdel Azim Ibrahim,Mahmoud Fayez,Mohammed Al-Nazawi +5 more
TL;DR: A fundamental knowledge gap question is to be resolved by evaluating the differences in biological and pathogenic aspects of SARS‐CoV‐2 and the changes in Sars‐Co V‐2 in comparison with the two prior major COV epidemics, SARS and Middle East respiratory syndrome (MERS) coronaviruses.
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