Literature DB >> 32511296

Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia.

Jessica E Manning1, Jennifer A Bohl1, Sreyngim Lay1, Sophana Chea1, Ly Sovann2, Yi Sengdoeurn2, Seng Heng2, Chan Vuthy2, Katrina Kalantar3, Vida Ahyong4, Michelle Tan4, Jonathan Sheu3, Cristina M Tato4, Joseph L DeRisi4, Laurence Baril5, Veasna Duong6, Philippe Dussart6, Erik A Karlsson6.   

Abstract

Rapid production and publication of pathogen genome sequences during emerging disease outbreaks provide crucial public health information. In resource-limited settings, especially near an outbreak epicenter, conventional deep sequencing or bioinformatics are often challenging. Here we successfully used metagenomic next generation sequencing on an iSeq100 Illumina platform paired with an open-source bioinformatics pipeline to quickly characterize Cambodia's first case of COVID-2019.

Entities:  

Keywords:  COVID-19; SARS-CoV-2; coronavirus; sequencing; unbiased metagenomics

Year:  2020        PMID： 32511296      PMCID： PMC7217139          DOI： 10.1101/2020.03.02.968818

Source DB:  PubMed          Journal:  bioRxiv


  9 in total

1.  A Novel Coronavirus Emerging in China - Key Questions for Impact Assessment.

Authors:  Vincent J Munster; Marion Koopmans; Neeltje van Doremalen; Debby van Riel; Emmie de Wit
Journal:  N Engl J Med       Date:  2020-01-24       Impact factor: 91.245

Review 2.  Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection.

Authors:  Wei Gu; Steve Miller; Charles Y Chiu
Journal:  Annu Rev Pathol       Date:  2018-10-24       Impact factor: 23.472

3.  Pathogen Genomics in Public Health.

Authors:  Gregory L Armstrong; Duncan R MacCannell; Jill Taylor; Heather A Carleton; Elizabeth B Neuhaus; Richard S Bradbury; James E Posey; Marta Gwinn
Journal:  N Engl J Med       Date:  2019-12-26       Impact factor: 91.245

4.  GitHub Statistics as a Measure of the Impact of Open-Source Bioinformatics Software.

Authors:  Mikhail G Dozmorov
Journal:  Front Bioeng Biotechnol       Date:  2018-12-18

5.  A pneumonia outbreak associated with a new coronavirus of probable bat origin.

Authors:  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; Mei-Qin Liu; Ying Chen; Xu-Rui Shen; Xi Wang; Xiao-Shuang Zheng; Kai Zhao; Quan-Jiao Chen; Fei Deng; Lin-Lin Liu; Bing Yan; Fa-Xian Zhan; Yan-Yi Wang; Geng-Fu Xiao; Zheng-Li Shi
Journal:  Nature       Date:  2020-02-03       Impact factor: 69.504

6.  Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia.

Authors:  Qun Li; Xuhua Guan; Peng Wu; Xiaoye Wang; Lei Zhou; Yeqing Tong; Ruiqi Ren; Kathy S M Leung; Eric H Y Lau; Jessica Y Wong; Xuesen Xing; Nijuan Xiang; Yang Wu; Chao Li; Qi Chen; Dan Li; Tian Liu; Jing Zhao; Man Liu; Wenxiao Tu; Chuding Chen; Lianmei Jin; Rui Yang; Qi Wang; Suhua Zhou; Rui Wang; Hui Liu; Yinbo Luo; Yuan Liu; Ge Shao; Huan Li; Zhongfa Tao; Yang Yang; Zhiqiang Deng; Boxi Liu; Zhitao Ma; Yanping Zhang; Guoqing Shi; Tommy T Y Lam; Joseph T Wu; George F Gao; Benjamin J Cowling; Bo Yang; Gabriel M Leung; Zijian Feng
Journal:  N Engl J Med       Date:  2020-01-29       Impact factor: 176.079

7.  Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance.

Authors:  Xianding Deng; Asmeeta Achari; Scot Federman; Guixia Yu; Sneha Somasekar; Inês Bártolo; Shigeo Yagi; Placide Mbala-Kingebeni; Jimmy Kapetshi; Steve Ahuka-Mundeke; Jean-Jacques Muyembe-Tamfum; Asim A Ahmed; Vijay Ganesh; Manasi Tamhankar; Jean L Patterson; Nicaise Ndembi; Dora Mbanya; Lazare Kaptue; Carole McArthur; José E Muñoz-Medina; Cesar R Gonzalez-Bonilla; Susana López; Carlos F Arias; Shaun Arevalo; Steve Miller; Mars Stone; Michael Busch; Kristina Hsieh; Sharon Messenger; Debra A Wadford; Mary Rodgers; Gavin Cloherty; Nuno R Faria; Julien Thézé; Oliver G Pybus; Zoraima Neto; Joana Morais; Nuno Taveira; John R Hackett; Charles Y Chiu
Journal:  Nat Microbiol       Date:  2020-01-13       Impact factor: 17.745

8.  Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak.

Authors:  Stephen K Gire; Augustine Goba; Kristian G Andersen; Rachel S G Sealfon; Daniel J Park; Lansana Kanneh; Simbirie Jalloh; Mambu Momoh; Mohamed Fullah; Gytis Dudas; Shirlee Wohl; Lina M Moses; Nathan L Yozwiak; Sarah Winnicki; Christian B Matranga; Christine M Malboeuf; James Qu; Adrianne D Gladden; Stephen F Schaffner; Xiao Yang; Pan-Pan Jiang; Mahan Nekoui; Andres Colubri; Moinya Ruth Coomber; Mbalu Fonnie; Alex Moigboi; Michael Gbakie; Fatima K Kamara; Veronica Tucker; Edwin Konuwa; Sidiki Saffa; Josephine Sellu; Abdul Azziz Jalloh; Alice Kovoma; James Koninga; Ibrahim Mustapha; Kandeh Kargbo; Momoh Foday; Mohamed Yillah; Franklyn Kanneh; Willie Robert; James L B Massally; Sinéad B Chapman; James Bochicchio; Cheryl Murphy; Chad Nusbaum; Sarah Young; Bruce W Birren; Donald S Grant; John S Scheiffelin; Eric S Lander; Christian Happi; Sahr M Gevao; Andreas Gnirke; Andrew Rambaut; Robert F Garry; S Humarr Khan; Pardis C Sabeti
Journal:  Science       Date:  2014-08-28       Impact factor: 47.728

9.  Nanopore Sequencing as a Rapidly Deployable Ebola Outbreak Tool.

Authors:  Thomas Hoenen; Allison Groseth; Kyle Rosenke; Robert J Fischer; Andreas Hoenen; Seth D Judson; Cynthia Martellaro; Darryl Falzarano; Andrea Marzi; R Burke Squires; Kurt R Wollenberg; Emmie de Wit; Joseph Prescott; David Safronetz; Neeltje van Doremalen; Trenton Bushmaker; Friederike Feldmann; Kristin McNally; Fatorma K Bolay; Barry Fields; Tara Sealy; Mark Rayfield; Stuart T Nichol; Kathryn C Zoon; Moses Massaquoi; Vincent J Munster; Heinz Feldmann
Journal:  Emerg Infect Dis       Date:  2016-02       Impact factor: 6.883
  9 in total

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