Everything you need to know about the data

We strongly believe not only in making data open, but also in making it useful to other people.

To that end, we've done our best to document where these data come from, what they mean, and any known limitations about how they should be used.

Think we're missing something? Please let us know at [email protected]

Data overview

Current version:
CViSB version 1.1.0
updated 30 November 2020
View all release notes

Where do our data come from?

The majority of our data is provided to CViSB through a partnership with the Kenema Government hospital (KGH) in Sierra Leone. KGH is home to Sierra Leone's only Lassa fever isolation ward, which was used during the 2014-2016 West African Ebola outbreak to treat Ebola as well. Read more about the isolation ward in the height of the Ebola outbreak .

Schema

Building off of schema.org's data models, we created schema to organize and standardize our patient, sample, dataset, experiment, and other related data.

Data dictionaries

... will be coming soon. In the meantime, peruse our schema, which contain information about how we define variables in our datasets.

Cohort definition

Patients are grouped into four cohorts: Ebola, Lassa, Control, or Unknown. People in the Ebola or Lassa group are not necessarily infected with the virus. Rather, they are either patients suspected of infection (pending diagnostic confirmation), or contacts of these patients who have suspected exposure to the virus. For specific analyses, you will need to decide how to define the cohort.

Outcome definition

Patients are grouped into five outcomes: survivor, dead, contact, control, or unknown.

  • Survivors are patients who were alive at least 10 days after presenting at a treatment center.
  • Dead are patients who have a confirmed death related to the virus.
  • Contacts are people who have been exposed to a patient infected with a virus.
  • Controls are healthy people who show no symptoms of infection.
  • Unknowns are people whose status is not known 10 or more days after presentation.

Limitations

Please note that this data is still based on work in progress and should be considered preliminary. If you intend to include any of these data in publications, please let us know – otherwise please feel free to download and use without restrictions. We have shared this data with the hope that people will download and use it, as well as scrutinize it so we can improve our methods and analyses. Please contact us if you have any questions or comments.

Citing the CViSB Data Portal

To reference data from the Center for Viral Systems Biology Data Portal, please cite the Center for Viral Systems Biology:

The Center for Viral Systems Biology, 2021, "Center for Viral Systems Biology data", https://data.cvisb.org/, V1.1.0.

Citing individual data sources

The data in the CViSB Data Portal is a mixture of data collected by our consortium, data contributed by our partners, and publicly available data on Lassa and Ebola. Some of the data has been published and others are works in progress. Individual data sources can be cited as:

Systems Serology data

Caroline Atyeo et al.Immunity2020, 53, 3, 524-532.e4.

rapid diagnostics data

Viral Hemorrhagic Fever Consortium / Kenema Government Hospital, 2021, https://data.cvisb.org/dataset/rapid-diagnostics-vhf. (unpublished)

vitals data

Viral Hemorrhagic Fever Consortium / Kenema Government Hospital, 2021, https://data.cvisb.org/dataset/vitals-vhf. (unpublished)

blood chemistry data

Viral Hemorrhagic Fever Consortium / Kenema Government Hospital, 2021, https://data.cvisb.org/dataset/blood-chemistry-vhf. (unpublished)

RT-PCR data

Viral Hemorrhagic Fever Consortium / Kenema Government Hospital, 2021, https://data.cvisb.org/dataset/rtpcr-vhf. (unpublished)

blood counts data

Viral Hemorrhagic Fever Consortium / Kenema Government Hospital, 2021, https://data.cvisb.org/dataset/blood-counts-vhf. (unpublished)

RT-PCR data

Caroline Atyeo et al.Immunity2020, 53, 3, 524-532.e4.

Ebola virus sequencing data

Armando Arias et al.Virus evolution2016, 2, 1, vew016.
Daniel J Park et al.Cell2015, 161, 7, 1516-26.
Miles W Carroll et al.Nature2015, 524, 7563, 97-101.
Yi-Gang Tong et al.Nature2015, 524, 7563, 93-6.
Jason T Ladner et al.Cell host & microbe2015, 18, 6, 659-69.
Joshua Quick et al.Nature2016, 530, 7589, 228-232.
Stephen K Gire et al.Science (New York, N.Y.)2014, 345, 6202, 1369-72.
Etienne Simon-Loriere et al.Nature2015, 524, 7563, 102-4.
Placide Mbala-Kingebeni et al.The Lancet. Infectious diseases2019, 19, 6, 648-657.
Tao Li et al.JCI insight2017, 2, 15, e88333.
Tao Jiang et al.The Journal of infectious diseases2017, 215, 7, 1107-1110.
Saskia L Smits et al.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin2015, 20, 40, 10.2807/1560-7917.ES.2015.20.40.30035.
Jeffrey R Kugelman et al.Emerging infectious diseases2015, 21, 7, 1135-43.
Serena A Carroll et al.Journal of virology2013, 87, 5, 2608-16.
David J Blackley et al.Science advances2016, 2, 4, e1600378.
Placide Mbala-Kingebeni et al.The Lancet. Infectious diseases2019, 19, 6, 641-647.
Tony Li et al.Journal of clinical microbiology2019, 57, 9, e00827-19.
Onikepe A Folarin et al.The Journal of infectious diseases2016, 214, suppl 3, S102-S109.
Thomas Hoenen et al.Emerging infectious diseases2016, 22, 2, 331-4.
Kayla G Barnes et al.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America2017, 65, 8, 1400-1403.
Shannon L M Whitmer et al.The Journal of infectious diseases2016, 214, suppl 3, S333-S341.
Andrea Marzi et al.Cell reports2018, 23, 6, 1806-1816.
M B DeSilva et al.Epidemiology and infection2019, 147, e88.
Alexander L Greninger et al.Genome medicine2015, 7, 99.
Suzanne E Mate et al.The New England journal of medicine2015, 373, 25, 2448-54.
Suzanne E Mate et al.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America2018, 67, 7, 1147-1149.
Gilda Grard et al.The Journal of infectious diseases2011, 204 Suppl 3, Suppl 3, S776-84.
Sylvain Baize et al.The New England journal of medicine2014, 371, 15, 1418-25.
Gaël D Maganga et al.The New England journal of medicine2014, 371, 22, 2083-91.
Jens H Kuhn et al.Genome announcements2014, 2, 6, e01178-14.
Concetta Castilletti et al.Genome announcements2015, 3, 3, e00639-15.
Shanmuga Sozhamannan et al.Viruses2015, 7, 6, 3130-54.
César G Albariño et al.Virology2015, 484, 259-64.
Maria R Capobianchi et al.Genome announcements2015, 3, 5, e01093-15.
Olamide K Oloniniyi et al.Journal of virological methods2017, 246, 8-14.
Emily Kainne Dokubo et al.The Lancet. Infectious diseases2018, 18, 9, 1015-1024.

Lassa virus sequencing data

Katherine J Siddle et al.The New England journal of medicine2018, 379, 18, 1745-1753.
Kristian G Andersen et al.Cell2015, 162, 4, 738-50.
L E Kafetzopoulou et al.Science (New York, N.Y.)2019, 363, 6422, 74-77.
Elisabeth Fichet-Calvet et al.Scientific reports2016, 6, 21977.
Tomasz A Leski et al.Emerging infectious diseases2015, 21, 4, 609-18.
M D Bowen et al.Journal of virology2000, 74, 15, 6992-7004.
Deborah U Ehichioya et al.Journal of clinical microbiology2011, 49, 3, 1157-61.
Olamide K Oloniniyi et al.PLoS neglected tropical diseases2018, 12, 11, e0006971.
Danny A Asogun et al.PLoS neglected tropical diseases2012, 6, 9, e1839.
David Coulibaly-N'Golo et al.PloS one2011, 6, 6, e20893.
Ayodeji Olayemi et al.Emerging infectious diseases2016, 22, 4, 694-7.
Stephan Olschläger et al.Journal of clinical microbiology2010, 48, 6, 2009-13.
Anges Yadouleton et al.Emerging microbes & infections2020, 9, 1, 1761-1770.
David Safronetz et al.Emerging infectious diseases2010, 16, 7, 1123-6.
Deborah U Ehichioya et al.Journal of virology2019, 93, 21, e00929-19.
Hayden C Metsky et al.Nature biotechnology2019, 37, 2, 160-168.
Ayodeji Olayemi et al.Scientific reports2016, 6, 25280.
B F Ardelli et al.Transactions of the Royal Society of Tropical Medicine and Hygiene2007, 101, 12, 1223-32.
David Safronetz et al.PLoS neglected tropical diseases2013, 7, 12, e2582.
A H Demby et al.Journal of clinical microbiology1994, 32, 12, 2898-903.
Leonce Kouadio et al.Emerging infectious diseases2015, 21, 8, 1481-3.
Simon Vieth et al.Virology2004, 318, 1, 153-68.
S Günther et al.The Journal of infectious diseases2001, 184, 3, 345-9.
Simon Vieth et al.Transactions of the Royal Society of Tropical Medicine and Hygiene2007, 101, 12, 1253-64.
Xavier Carnec et al.Journal of virology2011, 85, 22, 12093-7.
D D Auperin et al.Virology1989, 168, 2, 421-5.
Shannon L M Whitmer et al.Emerging infectious diseases2018, 24, 3, 599-602.
Junki Maruyama et al.mSphere2019, 4, 5, e00428-19.
Michael R Wiley et al.The Lancet. Infectious diseases2019, 19, 12, 1371-1378.
M Djavani et al.Virology1997, 235, 2, 414-8.
S Günther et al.Emerging infectious diseases2000, 6, 5, 466-76.
Emilie Lecompte et al.Emerging infectious diseases2006, 12, 12, 1971-4.
S Atkin et al.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin2009, 14, 10, 19145.
J C Clegg et al.Virus research1991, 18, 2-3, 151-64.
D D Auperin et al.Virology1986, 154, 1, 155-67.
J C Clegg et al.Virology1985, 144, 2, 363-72.
M D Bowen et al.Molecular phylogenetics and evolution1997, 8, 3, 301-16.