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Lassa Virus Sequencing virus sequencingLassaLassa virusLASV
Lassa Virus Sequencing
updated 13 February 2020
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.
How to cite
The Center for Viral Systems Biology, 2020, "Lassa Virus Sequencing", https://data.cvisb.org/lassa-virus-seq, V0.2.
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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
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
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