Weekly Epidemiological Report

September 2019 Week 39


Strengthening Regional Health Security: NCDC Hosts Cholera Genetic Sequencing Workshop for West Africa

Posted: 15-10-2019 11:12:17 AM

Nigeria and other countries in West Africa continue to experience outbreaks of cholera every year. Despite the reduction in cases in the last two years, these outbreaks continue to affect lives of people in Nigeria and other countries.While other neighbouring countries like Cameroun and Niger Republic have similarly recorded some progress in the elimination of cholera, the possible trans-border of cholera across Nigeria, Cameroun and Niger based on recurrent outbreaks at border communities remains a major source of concern with implications for regional health security.

As part of our goal to better understand the epidemiology of cholera in West Africa, scientists from Johns Hopkins University through the Global Taskforce for Cholera Control (GTFCC) organised a workshop at the NCDC National Reference Laboratory, Abuja.

The goal of this workshop was to carry out sequencing of cholera samples in order to identify if reported in the region are from a single V. cholerae introduction or if they resulted from multiple overlapping epidemics caused by multiple introductions of the organism over the last two years. In addition to scientists from NCDC’s National Reference Laboratory and network of laboratories, the workshop also had focal points for cholera (laboratory and epidemiology) from Cameroun and Niger Republic.

The outcomes of the workshop were:

1. Trained focal points of public health reference laboratories from Nigeria, Niger and Cameroun on sequencing V. cholerae O1 using the Oxford Nanopore MinION platform

2. Introduction to the Oxford Nanopore bioinformatics pipeline for V. cholerae O1 to assemble genomes and conduct basic phylogenetic analyses

3. Sequencing of isolates collected from 2015-2019 in all three countries

4. Combined genomic and epidemiologic information from all three countries to describe the regional outbreak dynamics, which will form the basis of a collaborative peer-reviewed manuscript

5. Developed first draft of a standard operating procedure for rapid identification and analysis of cholera transmission to be used in future surges of cases with the final aim of improving the regional response to outbreaks.

A major outcome from the workshop is the possibility to identify pathogens other than V. cholerae O1 which could be responsible for cholera outbreaks in Nigeria, Cameroun and Niger. This could lead to improved epidemic intelligence, patient care and inform public health policy.

NCDC remains committed to working closely with our counterparts in neighbouring countries for a better understanding of causative organisms leading to large outbreaks, and using this knowledge to improve preparedness and response activities.

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 108 suspected cases of Lassa Fever (LF) reported from 12 LGAs in 10 states & FCT (Edo – 66, Ondo – 25, Bauchi – 1, Plateau – 4, Gombe – 1, Benue – 1, Enugu – 2, Kebbi – 1, Abia – 3, FCT - 3 & Yobe – 1). There were 13 confirmed cases and two deaths were recorded


To date:

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

• A Lassa Fever National Environmental Response, coordinated by Federal Ministry of Environment in collaboration with NCDC and supported by WHO was carried out in Edo and Ondo states

• Implementation of targeted risk communication and enhanced surveillance activities in affected States


• 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 23 suspected cases of Cerebrospinal Meningitis (CSM) reported from 11 LGAs in five states (Cross River – 2, Kano – 1, Katsina – 18, Plateau – 1 & Yobe – 1). None was laboratory confirmed and one death was recorded


To date:

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


• Continue harmonisation of the national line list and SORMAS data

• Establish a mechanism for getting weekly feedback from states.

Yellow Fever

Key points

There were 116 suspected cases of Yellow Fever (YF) reported from 70 LGAs in 23 states & FCT. None was laboratory confirmed and two 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

• 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 campaign in Rivers, Ekiti & Anambra states in the fourth week of November 2019.


Key points

There were 31 suspected cases of Cholera reported from three LGAs in two states (Adamawa – 10 & Borno – 21). There were two laboratory confirmed cases and no death was recorded


To date:

• A Cholera multisectoral preparedness meeting was held with partners in Borno state

• 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 monitor non-reporting states.


Key points

There were 260 suspected cases of measles reported from 115 LGAs in 27 states and FCT. 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

• Following up with states still reporting above 50 cases


• Continue the review of measles surveillance data across the country

• Follow up with Katsina state on the next line of action

• Conduct measles surveillance guideline consolidation meeting from 15th – 17th October, 2019.


Key points

• There were three suspected cases of monkeypox reported from two LGAs in two states (Rivers – 1 & Lagos – 2). All of them were confirmed and no death was recorded


To date:

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

• Surveillance has been enhanced in all affected states


• Deploy Rapid Response Team to Akwa Ibom state to enhance surveillance activities.

• Dissemination of the reviewed case information form to all states.

Acute Flaccid Paralysis (AFP)

Key points

• There were 101 suspected cases of AFP reported from 86 LGAs in 31 states and FCT. None was laboratory confirmed and no death was recorded.

National Influenza Sentinel Surveillance

Key points

There were 53 processed samples positive for influenza, with 49 for influenza A, 3 for influenza B and 1 for influenza A&B.

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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