Plant Viral Metagenomic Analysis from a Preliminary Field Survey in Angola Reveals Complex Mixed Infections in Vegetable Crops

Abstract

Climatic changes are heavily affecting the sustainability of vegetable crops crucial for food supply worldwide, mainly in subtropical countries. One of the main threats to food security is the spread of diseases caused by plant viruses, favored by irregular rains and extreme temperatures, which reduce crop yield and quality. During a preliminary field survey carried out in two provinces of Angola in 2024, a few symptomatic plants of tomato, habanero pepper, common bean and a wild weed were sampled. These plants generally showed dwarfing, yellowing and leaf curl and were submitted to high-throughput sequencing to detect any viral agent. The evidence of mixed infections of several polyphagous viruses with RNA or DNA genomes, variously affecting the selected plants, was assessed from the sequence analysis and further confirmed for most samples by molecular tests, like (RT)-PCR or qPCR. Emerging polero-, begomo and tobamoviruses were denoted as infecting these plants. A novel, previously unknown carlavirus was also described in a wild weed. Most of those viruses are efficiently mechanically transmitted or airborne vehiculated by insect vectors. Although based on a limited number of samples, this study provides a first insight into the diversity of viruses infecting vegetable crops in Angola. It also highlights the pressing need for a broader monitoring to better understand virus distribution and epidemiology, and suggests the use of virus-free seeds to reduce the potential risk to crop production.