Ebola Virus Sequencing undefined

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updated 16 November 2020

Virus sequencing of acute Ebola patients from Sierra Leone, Liberia, Guinea, and other countries. Virus sequence data will be used to determine potential correlations between the infecting virus genome and patient survival, disease severity and development of sequelae. When multiple sequences are available for one patient, the virus has been sequenced from that patient at several points in time.

How to cite

The Center for Viral Systems Biology, 2020, "Ebola Virus Sequencing", https://data.cvisb.org/ebola-virus-seq, V0.3.

3,024

experiments

Curated alignments

Our virus sequencing datasets combine genomic sequences generated as part of our consortium with publicly available sequences. In addition to providing the raw data, we also curate sequences and provide the alignments to the broader community for downstream analyses.

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Ebola virus curated alignment

View alignment methodology

We periodically combine genomic sequences generated as part of our consortium with publicly available sequences. Our curated alignments do not include:

laboratory strains (adapted, passaged, recombinant, antiviral & vaccine experiments)
sequences without a timestamp
subsequent timepoints, if multiple timepoints are available
duplicates (when more than one sequence is available for a single strain)

Remaining sequences are trimmed to their coding regions, codon aligned using MAFFT and inspected manually. At this step we discard:

low quality sequences (manual curation)
incomplete sequences (<95% of (NP+VP35+VP40+GP+VP30+VP24+L) ORFs length)

ORFs are arranged in sense orientation as follows:

Ebola: NP -NNN- VP35 -NNN- VP40 -NNN- GP -NNN- VP30 -NNN- VP24 -NNN- L

Sources

percent of experiments cited in source

28%

Armando Arias et al.Virus Evol2016

12%

Daniel J Park et al.Cell2015

9%

Miles W Carroll et al.Nature2015

9%

Yi-Gang Tong et al.Nature2015

7%

Jason T Ladner et al.Cell Host Microbe2015

6%

Joshua Quick et al.Nature2016

5%

Stephen K Gire et al.Science2014

4%

Etienne Simon-Loriere et al.Nature2015

3%

Placide Mbala-Kingebeni et al.Lancet Infect Dis2019

3%

Tao Li et al.JCI Insight2017

3%

Tao Jiang et al.J Infect Dis2017

2%

Saskia L Smits et al.Euro Surveill2015

1%

Jeffrey R Kugelman et al.Emerg Infect Dis2015

1%

Serena A Carroll et al.J Virol2013

1%

David J Blackley et al.Sci Adv2016

1%

Placide Mbala-Kingebeni et al.Lancet Infect Dis2019

1%

Tony Li et al.J Clin Microbiol2019

1%

Onikepe A Folarin et al.J Infect Dis2016

1%

Thomas Hoenen et al.Emerg Infect Dis2016

1%

Kayla G Barnes et al.Clin Infect Dis2017

0%

Shannon L M Whitmer et al.J Infect Dis2016

0%

Andrea Marzi et al.Cell Rep2018

0%

M B DeSilva et al.Epidemiol Infect2019

0%

Alexander L Greninger et al.Genome Med2015

0%

Suzanne E Mate et al.N Engl J Med2015

0%

Suzanne E Mate et al.Clin Infect Dis2018

0%

Gilda Grard et al.J Infect Dis2011

0%

Sylvain Baize et al.N Engl J Med2014

0%

Gaël D Maganga et al.N Engl J Med2014

0%

Jens H Kuhn et al.Genome Announc2014

0%

Concetta Castilletti et al.Genome Announc2015

0%

Shanmuga Sozhamannan et al.Viruses2015

0%

César G Albariño et al.Virology2015

0%

Maria R Capobianchi et al.Genome Announc2015

0%

Olamide K Oloniniyi et al.J Virol Methods2017

0%

Emily Kainne Dokubo et al.Lancet Infect Dis2018

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