NCDC Weekly Epidemiological Report: Volume 9, No. 39: 23rd – 29th September, 2019

News and Press Release
Originally published
View original


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

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.