Apples (Malus domestica), one of Iran’s oldest cultivated fruit crops, hold considerable economic importance. In this study, 170 apple leaf samples representing various commercial cultivars were collected across the country. RT-PCR screening targeted five common apple-infecting viruses and two viroids: apple chlorotic leaf spot virus (ACLSV), apple stem pitting virus (ASPV), apple stem grooving virus (ASGV), apple green crinkle-associated virus (AGCaV), apple mosaic virus (ApMV), apple scar skin viroid (ASSVd), and hop stunt viroid (HSVd). To identify additional or novel agents, 40 RT-PCR-negative samples were pooled into two composite groups and analyzed using next-generation sequencing (NGS). NGS was also performed on individual samples with mixed infections to retrieve full genomes. RT-PCR confirmed the presence of ACLSV, ASPV, ASGV, AGCaV, ApMV, and HSVd. NGS further revealed three additional pathogens: citrus concave gum-associated virus (CCGaV), apple hammerhead viroid (AHVd), and apricot vein clearing-associated virus (AVCaV), which were subsequently detected across the collection by RT-PCR. AGCaV was most prevalent (47.6%), followed by ACLSV (45.8%), HSVd (27.6%), AVCaV (20.5%), ASGV (17%), AHVd (15.2%), ASPV (14.1%), CCGaV (4.7%), and ApMV (3.5%). Mixed infections occurred in 67% of samples. Phylogenetic analysis based on CP genes (ACLSV, ASGV, AGCaV) and full genomes (AVCaV, AHVd) clustered Iranian isolates together, suggesting a common origin. This is the first report in Iran of AGCaV, CCGaV, ApMV, and AVCaV in apple, and notably, the first global report of AVCaV in a non-Prunus host. The findings provide the first comprehensive assessment of the sanitary status of apple trees in Iran.

Despite its first description in 1977 and numerous reports of its presence in various plant species in many countries, the molecular information available in GenBank for artichoke Italian latent virus (AILV) is still limited to a single complete genome sequence (RNA1 and 2) of a grapevine isolate (AILV-V) and a partial portion of the RNA2 sequence from an isolate of unknown origin and host. Here, we report the results of molecular analyses conducted on the RNA2 of some AILV isolates, sequenced for the first time in this study, together with the first-time identification of AILV in a new host plant species, namely chard (Beta vulgaris subsp. vulgaris), associated with vein clearing and mottling symptoms on leaves. The different AILV isolates sequenced were from artichoke (AILV-C), gladiolus (AILV-G), Sonchus (AILV-S), and chard (AILV-B). At the molecular level, the sequencing results of the RNA2 segments showed that AILV-C, AILV-G, AILV-S, and AILV-B had a length of 4629 nt (excluding the 3′ terminal polyA tail), which is one nt shorter than that of the AILV-V reported in GenBank. A comparison of the RNA2 coding region sequences of all the isolates showed that AILV-V was the most divergent isolate, with the lowest sequence identities of 83.2% at the nucleotide level and 84.7% at the amino acid level. Putative intra-species sequence recombination sites were predicted among the AILV isolates, mainly involving the genomes of AILV-V, AILV-C, and AILV-B. This study adds insights into the variability of AILV and the occurrence of recombination that may condition plant infection.

Ornamental plants can be reservoirs of plant viruses, facilitating virus dissemination through international trade. In this bougainvillea study, 58 samples collected from six ornamental nurseries in Apulia (southern Italy) were screened for the presence of known bougainvillea-infecting viruses, using PCR assays. Among the viruses tested, only Bougainvillea chlorotic vein banding virus (BCVBV) was detected, occurring in five (8.6%) of the samples, whereas Impatiens necrotic spot virus (INSV), Clerodendron yellow mosaic virus (ClYMV), tomato yellow ring virus (TYRV), and cucumber mosaic virus (CMV) were not detected. High-throughput sequencing (HTS) of one BCVBV-positive sample (O54) enabled reconstruction of a complete viral genome, designated BCVBV Mini-Thai (GenBank accession no. PQ682517). A second HTS analysis of a pooled set of PCR-negative samples revealed a genetically distinct BCVBV isolate that was not detected by PCR using previously published primers. The complete genome of this isolate was reconstructed through contig assembly and gap-filling PCR using newly designed primers, and was named BCVBV Apulia 1 (PQ682518). The genome of Mini-Thai was 8,822 nucleotides long, and had high nucleotide (98.5%) and amino acid (98.7%) similarities with the Malaysian isolate BCVBV-UKM. In contrast, BCVBV Apulia 1 (PQ682518) was 8,694 nucleotides long and had greatest nucleotide similarity (81.6%) with the Brazilian isolate BCVBV UNB-01, with 84.0% amino acid similarity in the polyprotein. Both isolates had typical Badnavirus genome organization, with four open reading frames, and clustered in distinct phylogenetic clades. Further screening of the 58 collected samples using primers designed on the Apulia 1 isolate detected seven (12.1%) additional infected samples. A primer set targeting conserved genomic regions was also developed, enabling detection of both isolates. This report is the first detection of BCVBV in Italy and Europe, and also reveals the presence of a genetically divergent isolate of this virus.

A survey was conducted in Bosnia and Herzegovina in 2023, to investigate the presence of several important viruses affecting cereals, particularly those associated to cereal yellow dwarf viruses (CYDVs) and barley yellow dwarf viruses (BYDVs). Sixty leaf samples were collected, including 47 from maize plants (Zea mays L.) and 13 from barley plants (Hordeum vulgare L.), from across four grain-producing regions (Odzak, Sarajevo, Gornji Vakuf and Ilidza). Assessments for both groups of viruses, using ELISA and RT-PCR assays, detected CYDV in one maize sample (hybrid BC 418B) out of the 60 samples assessed. Nucleotide sequence analysis of the RT-PCR amplicon (2476 bp) of Bosnian isolate from maize hybrid BC418B (GenBank no. PV476203) showed that the isolate had 99.1% similarity with the CYDV RPS Mexican isolate (RPV-Mex-1; GenBank no. NC002198). This is the first report of the presence of CYDV-RPS in Bosnia and Herzegovina.