Lassa Virus Sequencing

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updated 25 November 2021

Virus sequencing of Lassa-infected humans and rodents from Nigeria, 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, 2021, "Lassa Virus Sequencing", https://data.cvisb.org/lassa-virus-seq, V0.4.

1,932

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.

Download the alignments

Lassa virus L-Z curated alignment

Lassa virus NP-GP 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)
sequences from identified hospital epidemics

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 (GP+NP) or (Z+L) ORFs length)

ORFs are arranged in sense orientation as follows:

Lassa S segment: NP -NNN- GP

Lassa L segment: L -NNN- Z

Sources

percent of experiments cited in source

24%

Katherine J Siddle et al.N Engl J Med2018

21%

Kristian G Andersen et al.Cell2015

19%

L E Kafetzopoulou et al.Science2019

8%

Elisabeth Fichet-Calvet et al.Sci Rep2016

4%

Tomasz A Leski et al.Emerg Infect Dis2015

4%

M D Bowen et al.J Virol2000

3%

Deborah U Ehichioya et al.J Clin Microbiol2011

2%

Olamide K Oloniniyi et al.PLoS Negl Trop Dis2018

2%

Danny A Asogun et al.PLoS Negl Trop Dis2012

2%

David Coulibaly-N'Golo et al.PLoS One2011

2%

Ayodeji Olayemi et al.Emerg Infect Dis2016

2%

Stephan Olschläger et al.J Clin Microbiol2010

1%

Anges Yadouleton et al.Emerg Microbes Infect2020

1%

David Safronetz et al.Emerg Infect Dis2010

1%

Deborah U Ehichioya et al.J Virol2019

1%

Hayden C Metsky et al.Nat Biotechnol2019

1%

Ayodeji Olayemi et al.Sci Rep2016

0%

B F Ardelli et al.Trans R Soc Trop Med Hyg2007

0%

David Safronetz et al.PLoS Negl Trop Dis2013

0%

A H Demby et al.J Clin Microbiol1994

0%

Leonce Kouadio et al.Emerg Infect Dis2015

0%

Umaru Bangura et al.Biology (Basel)2021

0%

Simon Vieth et al.Virology2004

0%

S Günther et al.J Infect Dis2001

0%

Simon Vieth et al.Trans R Soc Trop Med Hyg2007

0%

Xavier Carnec et al.J Virol2011

0%

D D Auperin et al.Virology1989

0%

Shannon L M Whitmer et al.Emerg Infect Dis2018

0%

Junki Maruyama et al.mSphere2019

0%

Michael R Wiley et al.Lancet Infect Dis2019

0%

M Djavani et al.Virology1997

0%

S Günther et al.Emerg Infect Dis2000

0%

Emilie Lecompte et al.Emerg Infect Dis2006

0%

S Atkin et al.Euro Surveill2009

0%

J C Clegg et al.Virus Res1991

0%

D D Auperin et al.Virology1986

0%

J C Clegg et al.Virology1985

0%

M D Bowen et al.Mol Phylogenet Evol1997

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