NCDC Weekly Epidemiological Report: Volume 9, No. 38: 16th – 22nd September, 2019

News and Press Release
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Building in-country Capacity for Genetic Sequencing: NCDC National Reference Laboratory

In 2018, Nigeria recorded a large outbreak of Lassa fever. As at the 29th of September 2019, 701 confirmed cases have been reported this year - more than the number of cases recorded in 2018. The Nigeria Centre for Disease Control (NCDC) continues to work closely with stakeholders, in improving knowledge on Lassa fever through research activities and epidemiological studies. One of these is in collaboration with the UK-Public Health Rapid Support Team (UK-PHRST) to identify other pathogens that may be causing illnesses similar to Lassa fever.

Lassa fever commonly presents with acute febrile illness. However, one critical question is “what pathogens are circulating that could be responsible for the systemic febrile illness among the over 1000 Lassa fever negative samples which met the case definition criteria for Lassa fever during the 2018 LF outbreak”?

NCDC and UK-PHRST have begun a study aimed at identifying the likely pathogen(s) circulating in Nigeria which are clinically indistinguishable from Lassa fever and responsible for significant disease burden during a Lassa fever virus outbreak. This innovation employs the use of TaqMan array card with pre-spotted single-plex real time PCR reactions with the ability to screen a single sample for up to 50 pathogens. Identified pathogens are being confirmed using MinIon sequencing. All testing and sequencing are done at the NCDC National Reference Laboratory.

When completed, one major benefit of this approach is the possibility of identifying a causative pathogen in Lassa-negative samples, which would allow recommendations and revisions of current testing algorithm. This could also lead to improved patient care, surveillance data and inform public health policy.

In addition to the contribution to science, this collaboration with UKPHRST is supporting the growth of in-country capacity for genetic sequencing in Nigeria and leadership by local experts.

Summary of Incidents

Ongoing Incidents are defined as confirmed cases where a national EOC or equivalent has been activated (EOC is currently activated for Yellow Fever)

Other incidents are those confirmed cases for which EOC is not activated.


  1. Information for this disease was retrieved from the Technical Working Group and Situation Reports

  2. Case Fatality Rate (CFR) for this disease is reported for confirmed cases only

  3. Information for this disease was retrieved from IDSR 002 data

  4. CFR for this disease is reported for total cases i.e. suspected + confirmed

  5. Information for sentinel influenza was retrieved from the laboratory