Despite the importance of potatoes to the Egyptian economy, which comprise 14% of Egypt's agricultural exports, (Elawady & Abdulkheir, 2015), virus diversity studies in the main production area, the Delta region, remain limited (Elwan et al., 2017), with only one study using high-throughput sequencing (HTS) exploring the threats more broadly (Elwan et al., 2023). This study aimed to use HTS to evaluate the presence of previously undiscovered viruses in most of the potato-producing areas in the Delta region. Diseased potato samples (three per location) were collected from 33 locations in the 2022 and 2023 cropping seasons, pooled (0.1g from each sample) and the total RNA was extracted (NucleoSpin® RNA Plant isolation kit; Macherey-Nagel, Germany). Illumina MiSeq libraries were prepared using the TruSeq® Stranded Total RNA Library Prep Plant kit (Illumina, USA). Sequence data is recorded under NCBI Bioproject: PRJNA1180791.

A new virus was detected only in Mansoura City (Sample 26, Dec 2022); in this field, the potate leaves were observed to have a mosaic pattern (Fig. 1). For this sample, Illumina sequencing generated 1,442,884,300 nt pair-end reads (NCBI, SRA: SRR30598214). Using the Angua pipeline, three viruses were identified in a mixed infection: alfalfa mosaic virus (AMV), pepper virus A (PepVA) and potato virus Y (PVY). Reanalysis in Geneious Prime® 2022.2.2 (medium sensitivity) revealed that 24 reads aligned with 91.4% identity to the AMV RNA3 segment of isolate FRE (GenBank Accession No. KY549685), 66 reads aligned with 83.5% identity to PepVA, isolate IND-SHM (MH725809) and 49 reads aligned with 93% identity to PVY, isolate Egypt7 (KY863549). While AMV and PVY aligned closely with Egyptian isolates (Elwan et al., 2017), this is the first record of PepVA in Egypt and the first in potatoes globally.