Targeted next generation sequencing for malaria molecular epidemiology in africa

Targeted next generation sequencing for malaria molecular epidemiology in Africa

The last decade has seen a revolution in sequencing technology. The advent of parallelized high-throughput sequencing methods has supported an explosion in the amount of data that can be generated with dramatic reductions in the per base cost of the sequencing. Laboratory and bioinformatic processes have been rapidly developing to allow these innovations to assess a variety of biologic questions, ranging from questions best answered by whole genome sequencing to those best understood by evaluating more samples at one or a few specific loci in the genome (i.e. targeted sequencing). For the most part, this sequencing work has been conducted in Europe, North America and Asia.

Timely and annotated targeted sequencing data can provide essential information directly usable by National Malaria Control Programmes (NMCP), as well as answer basic questions in malaria epidemiology and biology. Surveillance of drug resistance, assessing parasite migration, and understanding transmission routes are all areas where targeted sequencing can provide valuable biologic insights and inform malaria control. These approaches allow higher-throughput, sensitivity and quantification of mixed samples compared to previously used targeted Sanger sequencing methods. At the same time, the development of more inexpensive benchtop sequencers has the potential to change the penetration of next generation sequencing into African research institutions. However, there remain significant technical and computational challenges for such analyses and highlight a need for additional bioinformatics expertise given the wide applicability.

This Thematic Series of Malaria Journal aims to highlight the potential uses of parallelized high-throughput sequencing methods in a way that is accessible to malaria control programmes to fulfil the potential for understanding the molecular epidemiology of malaria in Africa. It highlights some of the questions that are important to programmes and the potential approaches to answer these questions. The hurdles for implementing these methods at African institutions will be partially addressed, as well as potential approaches for making these methodologies achievable and sustainable in Africa.

Guest Editor: Jonathan Juliano
Series published:  2019

1. Content Type:Meeting Report

   Targeted Next Generation Sequencing for malaria research in Africa: current status and outlook

   Targeted Next Generation Sequencing (TNGS) is an efficient and economical Next Generation Sequencing (NGS) platform and the preferred choice when specific genomic regions are of interest. So far, only institut...

   Authors:Anita Ghansah, Edwin Kamau, Alfred Amambua-Ngwa, Deus S. Ishengoma, Oumou Maiga-Ascofare, Lucas Amenga-Etego, Awa Deme, William Yavo, Milijaona Randrianarivelojosia, Lynette Isabella Ochola-Oyier, Gideon Kofi Helegbe, Jeffery Bailey, Michael Alifrangis and Abdoulaye Djimde

   Citation:Malaria Journal 2019 18:324

   Published on: 23 September 2019

   • ViewFull Text
    
   • ViewPDF
2. Content Type:Review

   Applying next-generation sequencing to track falciparum malaria in sub-Saharan Africa

   Next-generation sequencing (NGS) technologies are increasingly being used to address a diverse range of biological and epidemiological questions. The current understanding of malaria transmission dynamics and ...

   Authors:Sofonias K. Tessema, Jaishree Raman, Craig W. Duffy, Deus S. Ishengoma, Alfred Amambua-Ngwa and Bryan Greenhouse

   Citation:Malaria Journal 2019 18:268

   Published on: 3 September 2019

   • ViewFull Text
    
   • ViewPDF
3. Content Type:Opinion

   Deployment and utilization of next-generation sequencing of Plasmodium falciparum to guide anti-malarial drug policy decisions in sub-Saharan Africa: opportunities and challenges

   Parasite resistance against anti-malarial drugs is a major threat to the ongoing malaria control and elimination strategies. This is especially true since resistance to the currently recommended artemisinins a...

   Authors:Deus S. Ishengoma, Queen Saidi, Carol H. Sibley, Cally Roper and Michael Alifrangis

   Citation:Malaria Journal 2019 18:267

   Published on: 3 September 2019

   • ViewFull Text
    
   • ViewPDF