Geographic and Genomic Distribution of SARS-CoV-2 Mutations
Reads0
Chats0
TLDR
The analysis may facilitate custom-designed antiviral strategies based on the molecular specificities of SARS-CoV-2 in different patients and geographical locations and shows the prevalence of single nucleotide transitions as the major mutational type across the world.Abstract:
The novel respiratory disease COVID-19 has reached the status of worldwide pandemic and large efforts are currently being undertaken in molecularly characterizing the virus causing it, SARS-CoV-2. The genomic variability of SARS-CoV-2 specimens scattered across the globe can underly geographically specific etiological effects. In the present study, we gather the 48,635 SARS-CoV-2 complete genomes currently available thanks to the collection endeavor of the GISAID consortium and thousands of contributing laboratories. We analyzed and annotated all SARS-CoV-2 mutations compared with the reference Wuhan genome NC_045512.2, observing an average of 7.23 mutations per sample. Our analysis shows the prevalence of single nucleotide transitions as the major mutational type across the world. There exist at least three clades characterized by geographic and genomic specificity. In particular, clade G, prevalent in Europe, carries a D614G mutation in the Spike protein, which is responsible for the initial interaction of the virus with the host human cell. Our analysis may facilitate custom-designed antiviral strategies based on the molecular specificities of SARS-CoV-2 in different patients and geographical locations.read more
Citations
More filters
Journal ArticleDOI
Genomic evidence for reinfection with SARS-CoV-2: a case study.
Richard L. Tillett,Richard L. Tillett,Joel Sevinsky,Paul D. Hartley,Heather Kerwin,Natalie Crawford,Andrew Gorzalski,Chris Laverdure,Subhash C. Verma,Cyprian C. Rossetto,David Jackson,Megan J Farrell,Stephanie Van Hooser,Mark Pandori +13 more
TL;DR: The findings suggest that the patient was infected by SARS-CoV-2 on two separate occasions by a genetically distinct virus, suggesting that previous exposure to Sars-Cov-2 might not guarantee total immunity in all cases.
Journal ArticleDOI
What defines an efficacious COVID-19 vaccine? A review of the challenges assessing the clinical efficacy of vaccines against SARS-CoV-2.
Susanne H. Hodgson,Kushal Mansatta,Garry Mallett,Victoria Harris,Katherine R. W. Emary,Andrew J. Pollard +5 more
TL;DR: The challenges in assessing the efficacy of candidate SARS-CoV-2 vaccines are explored, the caveats needed to interpret reported efficacy endpoints are discussed, and insight is provided into answering the seemingly simple question, “Does this COVID-19 vaccine work?”
Journal ArticleDOI
D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization.
Drew Weissman,Mohamad-Gabriel Alameh,Thushan I de Silva,Paul Collini,Hailey Hornsby,Rebecca Brown,Celia C. LaBranche,Robert J. Edwards,Laura L. Sutherland,Sampa Santra,Katayoun Mansouri,Sophie M. C. Gobeil,Charlene McDanal,Norbert Pardi,Nick Hengartner,Paulo J.C. Lin,Ying Tam,Pamela A. Shaw,Mark G. Lewis,Carsten Boesler,Ugur Sahin,Priyamvada Acharya,Barton F. Haynes,Bette T. Korber,David C. Montefiori +24 more
TL;DR: Sera from Spike-immunized mice, nonhuman primates and humans were evaluated for neutralization of pseudoviruses bearing either D614 or G614 spike, and found the G614 pseudovirus was moderately more susceptible to neutralization.
Journal ArticleDOI
LY-CoV1404 (bebtelovimab) potently neutralizes SARS-CoV-2 variants
Kathryn Westendorf,Stefanie Zentelis,Lingshu Wang,Denisa Foster,Peter Edward Vaillancourt,Matthew Wiggin,Erica Lovett,R. van der Lee,Jorg Hendle,A. Pustilnik,J. Michael Sauder,Lucas Kraft,Yu Ri Hwang,Robert W. Siegel,Jinbiao Chen,Beverly A. Heinz,Richard E. Higgs,Nicole L. Kallewaard,Kevin R. Jepson,Rodrigo Goya,Maia A. Smith,D. W. Collins,Davide Pellacani,Ping Xiang,Valentine de Puyraimond,Marketa Ricicova,Lindsay DeVorkin,Caitlin Jean Pritchard,Aoise O’Neill,Kush Dalal,Pankaj Panwar,Harveer Singh Dhupar,Fabian A. Garces,Courtney A. Cohen,John M. Dye,Kathleen E Huie,Catherine V. Badger,Darwyn Kobasa,Jonathan Audet,J. J. Freitas,Saleema Hassanali,Ina E. Hughes,Luis Munoz,Holly C. Palma,Bharathi Ramamurthy,Robert W. Cross,Thomas W. Geisbert,Vineet Menacherry,Kumari G. Lokugamage,Viktoriya Borisevich,Iliana Lanz,Lisa Anderson,Payal Sipahimalani,Kizzmekia S. Corbett,Eun Sung Yang,Yi Zhang,Wei Shi,Tongqing Zhou,Misook Choe,John Misasi,Peter D. Kwong,Nancy J. Sullivan,Barney S. Graham,Tara L. Fernandez,Carl L. Hansen,Ester Falconer,John R. Mascola,Bryan Edward Jones,Bryan C. Barnhart +68 more
TL;DR: In this paper , the authors used a high-throughput B cell screening pipeline to identify a highly potent SARS-CoV-2 spike glycoprotein receptor binding domain (RBD)-specific antibody.
Posted ContentDOI
LY-CoV1404 (bebtelovimab) potently neutralizes SARS-CoV-2 variants
Kathryn Westendorf,Stefanie Žentelis,Denisa Foster,Peter Edward Vaillancourt,Wiggin M,Erica Lovett,van der Lee R,Jorg Hendle,A. Pustilnik,Sauder Jm,Lucas Kraft,Yuri Hwang,Robert W. Siegel,Chen J,Beverly A. Heinz,Richard E. Higgs,Kalleward N,Kevin R. Jepson,Rodrigo Goya,Maia A. Smith,David Collins,Davide Pellacani,Ping Xiang,de Puyraimond,Marketa Ricicova,Devorkin L,Pritchard C,O’Neill A,Dalal K,Panwar P,Dhupar H,Garces Fa,Courtney A. Cohen,John M. Dye,Kathleen E. Huie,Catherine V. Badger,Darwyn Kobasa,Darwyn Kobasa,Jonathan Audet,Jonathan Audet,Freitas Jj,Saleema Hassanali,Ina Hughes,Munoz L,Palma Hc,Bharathi Ramamurthy,Cross Rw,Cross Rw,Geisbert Tw,Geisbert Tw,Menacherry,Kumari G. Lokugamage,Borisevich,Lanz I,Lisa Anderson,Sipahimalani P,Kizzmekia S. Corbett,Lingshu Wang,Eun Sung Yang,Yanzhao Zhang,Wei Shi,Barney S. Graham,Mascola,Fernandez Tl,Carl L. Hansen,Ester Falconer,Bryan Edward Jones,Bryan C. Barnhart +67 more
TL;DR: The LY-CoV1404 (also known as bebtelovimab) is a highly potent, neutralizing, SARS CoV-2 spike glycoprotein receptor binding domain (RBD)-specific antibody identified from a convalescent COVID-19 patient sample, obtained approximately 60 days after symptom onset as mentioned in this paper.
References
More filters
Journal ArticleDOI
Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding.
Roujian Lu,Xiang Zhao,Juan Li,Peihua Niu,Bo Yang,Honglong Wu,Wenling Wang,Hao Song,Baoying Huang,Na Zhu,Yuhai Bi,Xuejun Ma,Faxian Zhan,Liang Wang,Tao Hu,Hong Zhou,Zhenhong Hu,Weimin Zhou,Li Zhao,Jing Chen,Yao Meng,Ji Wang,Yang Lin,Jianying Yuan,Zhihao Xie,Jinmin Ma,William J. Liu,Dayan Wang,Wenbo Xu,Edward C. Holmes,George F. Gao,George F. Gao,Guizhen Wu,Weijun Chen,Weifeng Shi,Wenjie Tan,Wenjie Tan +36 more
TL;DR: The phylogenetic analysis suggests that bats might be the original host of this virus, an animal sold at the seafood market in Wuhan might represent an intermediate host facilitating the emergence of the virus in humans.
Journal ArticleDOI
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
Alexander E. Gorbalenya,Susan C. Baker,Ralph S. Baric,Raoul J. de Groot,Christian Drosten,Anastasia A. Gulyaeva,Bart L. Haagmans,Chris Lauber,Andrey M. Leontovich,Benjamin W. Neuman,Dmitry Penzar,Stanley Perlman,Leo L.M. Poon,Dmitry V. Samborskiy,Igor A. Sidorov,Isabel Sola,John Ziebuhr +16 more
TL;DR: The independent zoonotic transmission of SARS-CoV and SARS -CoV-2 highlights the need for studying viruses at the species level to complement research focused on individual pathogenic viruses of immediate significance.
Journal ArticleDOI
The proximal origin of SARS-CoV-2.
Kristian G. Andersen,Kristian G. Andersen,Andrew Rambaut,W. Ian Lipkin,Edward C. Holmes,Robert F. Garry +5 more
TL;DR: It is shown that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus, and scenarios by which they could have arisen are discussed.
Journal ArticleDOI
Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors
Linlin Zhang,Daizong Lin,Xinyuanyuan Sun,Ute Curth,Christian Drosten,Lucie Sauerhering,Stephan Becker,Katharina Rox,Rolf Hilgenfeld +8 more
TL;DR: The pharmacokinetic characterization of the optimized inhibitor reveals a pronounced lung tropism and suitability for administration by the inhalative route and work that may provide a basis for development of anticoronaviral drugs.
Journal ArticleDOI
Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2.
Qihui Wang,Yanfang Zhang,Lili Wu,Sheng Niu,Sheng Niu,Chunli Song,Chunli Song,Zengyuan Zhang,Guangwen Lu,Chengpeng Qiao,Yu Hu,Yu Hu,Kwok-Yung Yuen,Qisheng Wang,Huan Zhou,Jinghua Yan,Jianxun Qi +16 more
TL;DR: The crystal structure of the C-terminal domain of SARS-CoV-2 (SARS- coV- 2-CTD) spike (S) protein in complex with human ACE2 (hACE2) is presented, which reveals a hACE2-binding mode similar overall to that observed for SARS -CoV.
Related Papers (5)
Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus.
Bette T. Korber,Will Fischer,Sandrasegaram Gnanakaran,Hyejin Yoon,James Theiler,Werner Abfalterer,Nick Hengartner,Elena E. Giorgi,Tanmoy Bhattacharya,Brian T. Foley,Kathryn M. Hastie,Matthew Parker,David G Partridge,Cariad Evans,Timothy M. Freeman,Thushan I de Silva,Adrienne Angyal,Rebecca Brown,Laura Carrilero,Luke R. Green,Luke R. Green,Luke R. Green,Danielle C. Groves,Katie Johnson,Alexander J Keeley,Benjamin B Lindsey,Paul J. Parsons,Mohammad Raza,Sarah Rowland-Jones,Nikki Smith,Rachel Tucker,Dennis Wang,Matthew Wyles,Charlene McDanal,Lautaro G. Perez,Haili Tang,Alex Moon-Walker,Alex Moon-Walker,Alex Moon-Walker,Sean P. J. Whelan,Celia C. LaBranche,Erica Ollmann Saphire,David C. Montefiori +42 more
A pneumonia outbreak associated with a new coronavirus of probable bat origin
Peng Zhou,Xing-Lou Yang,Xian Guang Wang,Ben Hu,Lei Zhang,Wei Zhang,Hao Rui Si,Yan Zhu,Bei Li,Chao Lin Huang,Hui-Dong Chen,Jing Chen,Yun Luo,Hua Guo,Ren Di Jiang,Meiqin Liu,Ying Chen,Xu Rui Shen,Xi Wang,Xiao Shuang Zheng,Kai Zhao,Quanjiao Chen,Fei Deng,Lin Lin Liu,Bing Yan,Fa Xian Zhan,Yan-Yi Wang,Gengfu Xiao,Zhengli Shi +28 more
GISAID: Global initiative on sharing all influenza data - from vision to reality.
Yuelong Shu,John W. McCauley +1 more