Weekly Epidemiological Report

September 2019 Week 38


Building in-country Capacity for Genetic Sequencing: NCDC National Reference Laboratory

Posted: 08-10-2019 10:53:35 AM

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

Lassa Fever

Key points

• There were 100 suspected cases of Lassa Fever (LF) reported from 14 LGAs in 10 states (Edo – 49, Ondo – 19, Ebonyi – 7, Bauchi – 5, Taraba – 8, Benue – 1, Kogi – 1, Enugu – 3, Delta – 1, Lagos – 3 & Abia - 3). There were seven confirmed cases and two deaths were recorded

• Data cleaning and validation revealed all three FCT cases were imported from neighbouring states and so it was removed from list of affected states


To date:

• National Lassa Fever multi-partner, multi-sectoral Technical Working Group (TWG) continues to coordinate the response activities at all levels

• Deployment of surge staff to Federal Medical Centre, Owo, Ondo state and Irrua Specialist Teaching Hospital, Edo state treatment centres

• Dissemination of reviewed case management and safe burial practices guidelines


• Implement phase 2 of rodent control measures in hotspot LGAs

• Conduct a meeting to finalise the LF psychosocial guideline meeting in October 2019

• Review LF case management, and surveillance tools and SOPs in October 2019

Cerebrospinal Meningitis (CSM)

Key points

There were 24 suspected cases of Cerebrospinal Meningitis (CSM) reported from 12 LGAs in five states (Cross River – 2, Ebonyi – 2, Katsina – 18, Kebbi – 1 & Yobe – 1). None was laboratory confirmed and no death was recorded


To date:

• The national CSM TWG meets weekly to review reports from states and plan appropriately


• Conduct After Action Review (AAR)

• Harmonise surveillance and laboratory data

• Establish a mechanism for getting weekly feedback from states

Yellow Fever

Key points

There were 89 suspected cases of Yellow Fever (YF) reported from 52 LGAs in 23 states. None was laboratory confirmed and five deaths were recorded


To date:

• A national multiagency YF Incident Management System (IMS) is coordinating response activities

• Offsite support is being provided to all affected states

• Preventive mass vaccination campaign is ongoing in all LGAs of Katsina state

• Harmonisation of surveillance and laboratory data as well as updating of SORMAS platform

• Operationalisation of the three new laboratories added to the YF laboratory network


• Continue on-site and off-site support to affected states

• Conduct preventive mass vaccination in Rivers, Ekiti and Anambra states in the fourth week of November, 2019

• Follow up with ICG request for the affected states

• Scale up risk communication activities, advisories and press release


Key points

There were 32 suspected cases of Cholera reported from four LGAs in two states (Adamawa – 21 & Borno – 11). There were 11 laboratory confirmed cases and no death was recorded


To date:

• The national Cholera TWG continues to coordinate activities in states in collaboration with the Federal Ministry of Water Resources (FMWR) and support from partners

• Adamawa state EOC continues to coordinate response activities with support from partners


• Follow up with states with active outbreak and monitoring of non-reporting states


Key points

There were 314 suspected cases of measles reported from 138 LGAs in 28 states. None was laboratory confirmed and no death was recorded


To date:

• The measles TWG is closely monitoring surveillance data and response activities across the country

• The TWG is working closely with NPHCDA towards measles Supplemental Immunization Activity in Nigeria


• Continue the review of measles surveillance data across the country

• Finalise measles surveillance guideline.


Key points

• There were six suspected cases of monkeypox reported in five LGAs in four states and FCT (Delta – 1, FCT – 1, Imo – 2, Rivers – 1 & Zamfara - 1) this week. There was one confirmed case from Rivers state and no death was recorded

• The cases from Delta and FCT were confirmed for chickenpox (Varicella Zoster Virus)


To date:

• The national monkeypox TWG is monitoring and coordinating response activities across the states

• Surveillance has been enhanced in all affected states

• Offsite support is being provided to the affected states

Acute Flaccid Paralysis (AFP)

Key points

• There were 107 suspected cases of AFP reported from 98 LGAs in 30 states and FCT. None was laboratory confirmed and no death was recorded

National Influenza Sentinel Surveillance

Timeliness and Completeness of Reports

Timeliness and Completeness of Reports by State

Highlight of the week

  • Summary of Incidents
  • Lassa Fever
  • Cerebrospinal Meningitis (CSM)
  • Yellow Fever
  • Cholera
  • Measles
  • Monkeypox
  • Acute Flaccid Paralysis (AFP)
  • National Influenza Sentinel Surveillance
  • Timeliness and Completeness of Reports
  • Timeliness and Completeness of Reports by State

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