2018 Lassa virus sequencing in Nigeria

In response to the high number of Lassa fever cases in Nigeria from January - March of 2018, viral genome sequencing is being used to elucidate changes in the viral genome or transmission patterns that may account for this surge.

Here we report 14 new genomes (complete and partial) from patient plasma samples collected between January and March 2018 at Irrua Specialist Teaching Hospital, Irrua, Edo, Nigeria. Of these 14 samples, 12 come from Edo State, 1 from Kogi State and 1 from Ebonyi State. Samples were prepared and sequenced at the African Center of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer’s University, Ede, Nigeria using Illumina MiSeq sequencers.

These samples fall within known Lassa virus diversity in Nigeria and are well distributed throughout the tree (Figure 1). Although two samples from 2018 do cluster together on the tree, the estimated time to most recent common ancestor of these sequences makes it unlikely that this is a case of human-human transmission (Figure 1). More broadly, genetic diversity of these newly sequenced samples is consistent with multiple zoonotic transmission events and does not support sustained human transmission. Additional sequencing is ongoing to confirm these findings and further understand the mechanisms driving this increase in cases.

Figure 1. Time aware phylogeny of LASV S segment. Samples from 2018 as well as those recently shared from 2015-2016 are coloured by the region in which the patient resides. 2018 samples are those with full sample IDs, samples from 2015-16 are labelled with their accession names.

Data availability
Genome sequences for all samples are available here: https://storage.googleapis.com/sabeti-public/data_release/lasv_nga/round2/lasv-acegid-round2-fasta_only.tar.gz
These sequences are also available on NCBI under the accession numbers MH157026-MH157053.

Partners and collaborators
This work is part of ongoing research collaborations between several partners:
Irrua Specialist Teaching Hospital and Institute for Lassa Fever Research and Control (Irrua, Nigeria)
African Center of Excellence for Genomics of Infectious Disease (ACEGID Redeemer’s University, Ede, Nigeria)
Center for Viral Systems Biology (La Jolla, CA, USA)
Joint West Africa Research Group (Walter Reed Army Institute of Research, Bethesda, MD, USA)
Viral Hemorrhagic Fever Consortium (New Orleans, LA, USA)
Broad Institute of MIT and Harvard (Cambridge, MA, USA)
Harvard University (Cambridge, MA, USA)

Statement on continuing work and analyses prior to publication
These genomes are being shared pre-publication to help the research and public health communities respond to the current increase in Lassa cases. We encourage others to download, share, use, and analyze this data. Please note though that this data is still based on work in progress and should be considered preliminary. Our analyses of this data is ongoing and a publication communicating our findings on these and other published genomes is in preparation. If you intend to use these sequences prior to our publication, please contact us directly to coordinate. We will continue to release LASV genomes, prior to publication, as soon as they are generated to update the community.

Professor Christian Happi (Redeemer’s University, ACEGID): happic@run.edu.ng
Professor Pardis Sabeti (Harvard University, Broad Institute): pardis@broadinstitute.org
Philomena Eromon (Redeemer’s University, ACEGID): eromonp@run.edu.ng
Dr Katherine Siddle (Harvard University, Broad Institute): kjsiddle@broadinstitute.org

Update on data availability: Genome sequences for the 115 additional genomes from 2017-2018 recently reported in Siddle et al., NEJM, October 17 2018 are available here: https://storage.googleapis.com/sabeti-public/data_release/lasv_nga/round3/lasv-acegid-round3-fasta_only.tar.gz.