Detection and molecular analysis of shallot latent virus infecting Allium sativum in Zimbabwe

Abstract

The prevalence of phytoviruses threatens food security worldwide. A number of factors can contribute to phytoviruses remaining unidentified, including lack of resources and ignorance of their existence. This study aimed to identify and understand the molecular characteristics and phylogeny of shallot latent virus infecting garlic (Allium sativum) in Zimbabwe. Leaf samples, collected from garlic farms in and around Harare Metropolitan Province, Zimbabwe in 2015, 2016 and 2020, were tested for the presence of shallot latent virus (SLV) using DAS ELISA. 89 % of the samples tested positive for SLV. High throughput sequencing (HTS) was subsequently used to recover the genome of the virus isolate. RNA was extracted from SLV-positive samples and used in ribo-depleted RNA-Seq on an Illumina platform. Both de novo and reference assembly were used to generate the full-length genome of the SLV isolate q23-Manresa, accession number MG657357, infecting garlic in Zimbabwe. Its non-recombinant genome consists of 8423 nucleotides excluding the polyA tail. Three relationships were observed from the phylogenetic analyses of the isolate q23-Manresa to homologous non-recombinant SLV isolates identified in different parts of the world depending on the portion of the genome selected. The information generated in this study will contribute towards building a database of garlic-infecting viruses and developing surveillance strategies.