Early Results of Lassa Virus Sequencing and Implications for Current Outbreak Response in Nigeria

The Nigeria Centre for Disease Control continues to lead a multi-agency, multi-partner response to the on-going Lassa fever outbreak in Nigeria. The response is now gathering steam with an escalation of efforts to control spread in all the foci of infections across the country. A critical aspect of outbreak control is research, to rapidly understand the drivers of infection and opportunities for control.


A relatively new tool available to epidemiologists and researchers is the use of whole genome sequencing during outbreaks. Real-time sequencing of viruses can reveal crucial details that contribute to the understanding and the control of infectious disease outbreaks. It is now possible to resolve chains of transmission to a level of detail otherwise unachievable using traditional methods.

  Lassa Fever Cell

Researchers at the Irrua Specialist Teaching Hospital, Edo State, in collaboration with partners from the Bernhard-Nocht Institute for Tropical Medicine (Germany), Public Health England, the University of Liverpool and others (see below) have deployed real-time sequencing of Lassa fever viruses from the on-going outbreak to learn key lessons to influence control efforts. The real-time availability of sequencing information for the current 2018 Lassa fever viruses will support the response to the on-going Lassa fever outbreak.

On the 10th March 2018, the analysis of a first set of seven Lassa virus draft sequences derived from the blood of seven laboratory-confirmed Lassa fever patients from Edo, Ondo, Ebonyi, and Imo States was completed. In addition, 83 unpublished sequences obtained during previous years from various parts of Nigeria were made available for comparison with the sequences of the 2018 outbreak. From the analysis, of these results, we can draw the following preliminary conclusions:

• No new virus lineages have so far been detected, meaning that the circulating viruses appear to be very similar to the viruses from previous years;

• Lassa fever cases appear to be mostly caused by viruses that are not epidemiologically linked;

• The viruses circulating in 2018 appear to originate from the pool of lineages and strains known to be circulating in Nigeria and are consistent with previous outbreaks;

• The most likely route of transmission continues to be spill over of viruses from the rodent reservoir to humans rather than extensive human-to-human transmission.

The most important question being investigated at the moment is what has caused an outbreak of this magnitude, at this time? One of the possible answers to this question is the emergence of a new Lassa virus lineage or strain with increased virulence or transmissibility. Evidence from this work, although limited to seven viruses at the moment suggests that this is unlikely to be the case.

Over the last year, the Nigeria Centre for Disease Control has improved its disease surveillance, detection and response system. This includes the operationalisation of the National Reference Laboratory in Abuja, to add to existing diagnostic capacity, with its capacity to test for Lassa fever in ISTH and Lagos University Teaching Hospital (LUTH). According to Chief Executive Office, Dr. Chikwe Ihekweazu, “As the system continues to be strengthened, there is likely to be an increase in the number of cases detected and reported. Sequencing provides an exciting additional tool for the outbreak response. As we learn more, we become better equipped to respond.”

To support the public health response as well as the development and evaluation of Lassa fever diagnostics or therapeutics, the researchers are sharing the sequences via the website virological.org.

The NCDC would like to thank the following institutions and partners for their continued support to the Government of Nigeria:

• Irrua Specialist Teaching Hospital (ISTH), Institute of Lassa Fever Research and Control (ILFRC), Irrua, Edo State, Nigeria (Prof. Sylvanus Okogbenin, Dr. Ephraim Ogbaini, Dr. Adomeh Donatus)

• Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany (Prof. Stephan Günther, Liana Kafetzopoulou, Dr. Deborah Ehichioya, Dr. Meike Pahlmann, Dr. Lisa Oestereich, Dr. Sophie Duraffour, Anke Thielebein, Julia Hinzmann)

• Public Health England (PHE), Salisbury, United Kingdom (Prof. Miles Carroll, Liana Kafetzopoulou, Dr. Steven Pullan, Dr. Richard Vipond, Dr. Roger Hewson)

• KU Leuven, Leuven, Belgium (Dr. Philippe Lemey)

• University of Liverpool, United Kingdom (Dr. Julian Hiscox)

• World Health Organisation (WHO)

Posted on: 12/03/2018