High-Throughput Sequencing Application in the Diagnosis and Discovery of Plant-Infecting Viruses in Africa, A Decade Later

Abstract

High-throughput sequencing (HTS) application in the field of plant virology started in 2009 and has proven very successful for virus discovery and detection of viruses already known. Plant virology is still a developing science in most of Africa; the number of HTS-related studies published in the scientific literature has been increasing over the years as a result of successful collaborations. Studies using HTS to identify plant-infecting viruses have been conducted in 20 African countries, of which Kenya, South Africa and Tanzania share the most published papers. At least 29 host plants, including various agricultural economically important crops, ornamentals and medicinal plants, have been used in viromics analyses and have resulted in the detection of previously known viruses and novel ones from almost any host. Knowing that the effectiveness of any management program requires knowledge on the types, distribution, incidence, and genetic of the virus-causing disease, integrating HTS and efficient bioinformatics tools in plant virology research projects conducted in Africa is a matter of the utmost importance towards achieving and maintaining sustainable food security.

Keywords: 454 pyrosequencing; Illumina HiSeq; Illumina MiSeq; Maize; cassava; common bean; cowpea; food security; plant virology; sweet potato.

Figure 1

African countries that have been mentioned in high-throughput sequencing (HTS) studies related to the detection and diagnosis of plant-infecting viruses.

Figure 2

Host plants families that have been subjected to HTS for detection or diagnosis of plant-infecting virus.