Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 Áine O’Toole1,$,*, Verity Hill1*, Oliver G. Pybus2, Alexander Watts3,4, Isaac I. Bogoch5,6, Kamran Khan3,4,5, Jane P. Messina7, The COVID-19 Genomics UK (COG-UK) consortium8, Network for Genomic Surveillance in South Africa (NGS-SA)9, Brazil-UK CADDE Genomic Network10, Houriiyah Tegally11, Richard R Lessells11, Jennifer Giandhari11, Sureshnee Pillay11, Kefentse Arnold Tumedi13, Gape Nyepetsi14, Malebogo Kebabonye15, Maitshwarelo Matsheka13, Madisa Mine14, Sima Tokajian16, Hamad Hassan17, Tamara Salloum18, Georgi Merhi18, Jad Koweyes18, Jemma L Geoghegan19,20, Joep de Ligt20, Xiaoyun Ren20, Matthew Storey20, Nikki E Freed21,Chitra Pattabiraman22, Pramada Prasad22, Anita S Desai22, Ravi Vasanthapuram22,Thomas F. Schulz23, Lars Steinbrück23, Tanja Stadler24, Swiss Viollier Sequencing Consortium25, Antonio Parisi26, Angelica Bianco26, Darío García de Viedma27,28,29, Sergio Buenestado-Serrano27,28, Vítor Borges30, Joana Isidro30, Sílvia Duarte31, João Paulo Gomes30, Neta S. Zuckerman32, Michal Mandelboim32, Orna Mor32, Torsten Seemann33, Alicia Arnott34, Jenny Draper34, Mailie Gall34, William Rawlinson35, Ira Deveson36, Sanmarié Schlebusch37, Jamie McMahon37, Lex Leong38, Chuan Kok Lim38,Maria Chironna39, Daniela Laconsole39, Antonin Bal40, Laurence Josset40, Edward Holmes41, Kirsten St George42, Erica Lasek-Nesselquist42, Reina S. Sikkema43, Bas B. Oude Munnink43, Marion Koopmans43, Mia Brytting44, V. Sudha Rani45, S. Pavani45, Teemu Smura46, Albert Heim47, Satu Kurkela48, Massab Umair52, Muhammad Salman52, Barbara Bartolini53, Martina Rueca53, Christian Drosten54, Thorsten Wolff56, Olin Silander21, Dirk Eggink59, Chantal Reusken59, Harry Vennema59, Aekyung Park60, SEARCH Alliance San Diego48, National Virus Reference Laboratory49, SeqCOVID-Spain50, Danish Covid-19 Genome Consortium (DCGC)55, Communicable Diseases Genomic Network (CDGN)57, Dutch National SARS-CoV-2 surveillance program58,#, Division of Emerging Infectious Diseases KDCA60, Tulio de Oliveira11, Nuno R. Faria2,12, Andrew Rambaut1, Moritz U. G. Kraemer Wellcome Open Research. 2021 May 19;6:121. doi: 10.12688/wellcomeopenres.16661.1. eCollection 2021.
The power and limitations of genomics to track COVID-19 outbreaks: a case study from New Zealand. Jemma L Geoghegan, Jordan Douglas, Xiaoyun Ren, Matt Storey, James Hadfield, Olin K Silander, Nikki E Freed, Lauren Jelley, Sarah Jefferies, Jillian Sherwood, Shevaun Paine, Sue Huang, Andrew Sporle, Michael G Baker, David R Murdoch, Alexei J Drummond, David Welch, Colin R Simpson, Nigel French, Edward C Holmes, Joep de Ligt. Emerg Infect Dis. 2021 May; 27(5): 1317–1322.
Bac-PULCE: Bacterial Strain and AMR Profiling Using Long Reads via CRISPR Enrichment Andrea Sajuthi, Julia White, Gayle Ferguson, Nikki E. Freed, Olin K. Silander, Preprint at BioRxiv: doi: https://doi.org/10.1101/2020.09.30.320226
Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV2 using 1200 bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding Nikki E. Freed*, Markéta Vlková, Muhammad B. Faisal, Olin K. Silander*, July 2020
Method at Protocols.io: dx.doi.org/10.17504/protocols.io.bgggjttw
IDT now sells the 1200bp amplicon primer set as a pool: Product name: SARS-Cov2-Midnight-1200, 500rxn, IDT Product number : 10007184
*Co-Communicating author
Concordant geographic and genetic structure revealed by genotyping-by-sequencing in a New Zealand marine isopod. WS Pearman, SJ Wells, OK Silander, NE Freed, J Dale. Ecology and Evolution. 2020 Dec 2;10(24):13624-13639. DOI: 10.1002/ece3.6802
New tools for diet analyses: nanopore sequencing of metagenomic DNA from stomach contents to quantify diet in an invasive population of rats. Nikki E Freed*, William Pearman, Adam NH Smith, Georgia Breckell, James Dale, Olin K Silander*. Preprint at bioRxiv: https://www.biorxiv.org/content/10.1101/363622v3
Testing the advantages and disadvantages of short-and long-read eukaryotic metagenomics using simulated reads. WS Pearman*, NE Freed, OK Silander*. BMC Bioinformatics 21, 1-15, May 2020
Complete Genome Sequences of Nine Mycobacteriophages from New Zealand, Beatrix, Carthage, Daegal, Dulcie, Fancypants, Fenn, Inca, Naira, and Robyn. C. G. Davies, J. K. Wojtus, C. E. R. Gilligan, S. F. Latu, T. J. Manning, C. E. Meyer... “Microbiol Resour Announc, vol. 8, no. 20, p. 784, May 2019.
Complete Genome Sequences of Cluster A Mycobacteriophages BobSwaget, Fred313, KADY, Lokk, MyraDee, Stagni, and StepMih. K. A. Butela, S. M. R. Gurney, H. L. Hendrickson, J. M. LeBlanc-Straceski, A. M. Zimmerman, S. B. Conant, N. E. Freed, O. K. Silander, .... Genome Announc, vol. 5, no. 43, pp. e01182–17, Oct. 2017.
Creation of a dense transposon insertion library using bacterial conjugation in enterobacterial strains such as Escherichia coli or Shigella flexneri. NE Freed. Journal of Visualised Experiments (JoVE). Issue 127. DOI 10.3791/56216. 2017
Combining Tn-seq with comparative genomics identifies proteins uniquely essential in Shigella flexneri. NE Freed, D Bumann, O Silander, BMC Microbiology 16 (203), 1-14. 2016
A simple screen to identify promoters conferring high levels of phenotypic noise. NE Freed, OK Silander, B Stecher, A Böhm, WD Hardt, M Ackermann. PLoS Genet 4 (12), e1000307 41. 2008
Self-destructive cooperation mediated by phenotypic noise. M Ackermann, B Stecher, NE Freed, P Songhet, WD Hardt, M Doebeli. Nature 454 (7207), 987-990 18. 2008
Rapid detection and molecular serotyping of adenovirus by use of PCR followed by electrospray ionization mass spectrometry. LB Blyn, TA Hall, B Libby, R Ranken, R Sampath, K Rudnick, E Moradi, ... Journal of clinical microbiology 46 (2), 644-651432008
Diagnostic discrimination of live attenuated influenza vaccine strains and community-acquired pathogenic strains in clinical samples. NE Freed, CA Myers, KL Russell, EA Walter, M Irvine, RG Coon, ... Molecular and cellular probes 21 (2), 103-110112007
Transmission dynamics and prospective environmental sampling of adenovirus in a military recruit setting. KL Russell, MP Broderick, SE Franklin, LB Blyn, NE Freed, E Moradi, ... Journal of Infectious Diseases 194 (7), 877-8851172006
Co-infections of adenovirus species in previously vaccinated patients. GJ Vora, B Lin, K Gratwick, C Meador, C Hansen, C Tibbetts, DA Stenger, ... Emerg Infect Dis 12 (6), 921-930362006
Surveillance for febrile respiratory infections during Cobra Gold 2003. J Fuller, K Hanley, R Schultz, M Lewis, NE Freed, M Ellis, V Ngauy, ... Military medicine 171 (5), 357-35932006
Transmission dynamics and prospective environmental sampling of adenovirus in a military recruit setting.. GC GRAY, KL RUSSELL, MP BRODERICK, SE FRANKLIN, LB BLYN, ... The Journal of infectious diseases 194 (7) 2006
Rapid identification and strain-typing of respiratory pathogens for epidemic surveillance. DJ Ecker, R Sampath, LB Blyn, MW Eshoo, C Ivy, JA Ecker, B Libby, ... Proceedings of the National Academy of Sciences 102 (22), 8012-80171992005
Effectiveness of the 2003–2004 influenza vaccine among US military basic trainees: a year of suboptimal match between vaccine and circulating strain. KL Russell, MAK Ryan, A Hawksworth, NE Freed, M Irvine, LT Daum, ... Vaccine 23 (16), 1981-1985242005
Molecular analysis of adenovirus isolates from vaccinated and unvaccinated young adults. DA Blasiole, D Metzgar, LT Daum, MAK Ryan, J Wu, C Wills, CT Le, ... Journal of clinical microbiology 42 (4), 1686-1693512004
High throughput mass spectrometry for the identification and typing of biowarfare agents and pathogens associated with emerging infectious diseases: The TIGER approach. SA Hofstadler, DJ Ecker, LB Blyn, R Sampath, J Drader, Y Jiang, ... ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 227, U247-U248 2004