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Daffodils (family Amaryllidaceae, genus Narcissus) are important ornamental plants produced primarily for cut flowers. In 2019, daffodils sales in the US were $6.26 M (USDA-NASS, 2019). In May 2021, four symptomatic daffodil plants (Narcissus pseudonarcissus) were sampled from a flowerbed (

Citrus canker caused by Xanthomonas citri subsp. citri (syn. X. axonopodis pv. citri) was first reported in South Texas during the early 1900s, prompting quarantine and eradication programs by the federal government. Its last reported incidence in Texas was from two trees from Corpus Christi in 1943. In May 2016, USDA Animal and Plant Health Inspection Service-Plant Protection and Quarantine (PPQ) confirmed the presence of the Asiatic A strain, which is by far the most widespread and severe form infecting most citrus varieties, on two sour orange trees in a park in Houston. Subsequently, infected trees were detected in a nursery in Richmond (Fort Bend Co.) in August 2016 and in dooryard trees in Pearland (Brazoria Co.) in 2018. PPQ and Texas Department of Agriculture collected a combined 1,949 positive A strain samples from Harris, Fort Bend, and Brazoria Counties during May 2016 to January 2021. These findings resulted in seven active citrus canker quarantine zones being established in the Upper Gulf Coast area. The Texas Department of Agriculture is removing positive trees, and surveys are continuing.

Phytophthora ramorum, P. kernoviae, and P. melonis are each species of current regulatory concern in the United States, the United Kingdom, and other areas of the world. Ex-type material are cultures and duplicates of the type that was used to describe each species and that are deposited in additional culture collections. Using these type specimens as references is essential to designing correct molecular identification and diagnostic systems. Here, we report a whole genome sequence for the Ex-type material of P. ramorum, P. kernoviae, and P. melonis generated using high-throughput sequencing via the MinION third generation platform from Oxford Nanopore Technology. We assembled the quality filtered reads into contigs for each species. We assembled the continuous contigs of P. ramorum, P. kernoviae, and P. melonis (1,322, 545, and 2,091 contigs, respectively). The ab initio prediction of genes from these species reveals that there are 16,838, 12,793, and 34,580 genes in P. ramorum, P. kernoviae, and P. melonis, respectively. Of the 34,580 P. melonis genes, 10,164 genes were conserved among all three of these Phytophthora species which may include pathogenicity genes. We compared the ex-type of P. ramorum EU1 lineage assembly with another selected isolate of EU1 available at the National Center for Biotechnology Information and found 251,859 single nucleotide polymorphisms (SNPs) genome-wide; the comparison with the EU2 lineage genome isolate revealed 441,859 SNPs genome-wide. This genome resource of the ex-types of P. ramorum, and P. kernoviae is a significant contribution as these species are among the most important pathogens of regulatory concern in different regions of the world.

In October 2015, a Mexican lime exhibiting citrus canker symptoms was found by the USDA APHIS PPQ in a residential property in Rancho Viejo, Cameron County, Texas. Real-time PCR analysis detected the presence of Xanthomonas citri subsp. citri; USDA APHIS PPQ in Beltsville, MD confirmed this diagnosis. A delimiting survey was initiated and suspect leaf samples were collected and sent to the PPQ Beltsville lab for analysis. By October 2017, leaf samples from 197 trees were confirmed positive for citrus canker, all within a 5-mile radius; in addition, a further 59 symptomatic trees were found and all 256 infected trees (254 Mexican lime, one makrut lime, and one Ponderosa lemon) were removed. Survey data collected on stem lesions suggested the oldest lesions to be between 4 to 6 years old. A host-range study using 12 citrus varieties, including the major commercial varieties grown in Texas, were inoculated with crude leaf extracts from symptomatic leaves by leaf infiltration method. Mexican limes and alemow were the only citrus plants that developed definitive canker lesions. A combination of host range, serological, and molecular tests suggested that this isolate was different from the typical Asiatic strain and more similar to X. citri subsp. citri AW which was only previously reported from Florida on Mexican lime and alemow.

Four of 19 Prunus germplasm accessions hand carried from the Ukraine into the United States without authorization were found to be infected with Plum pox virus (PPV). Of the three isolates characterized, isolates UKR 44189 and UKR 44191 were confirmed to be isolates of PPV strain W, and UKR 44188 was confirmed to be an isolate of PPV strain D. UKR 44189 and UKR 44191 are very closely related to the PPV strain W isolate LV-145bt (HQ670748) from Latvia. Nucleotide and amino acid sequence identities between these three isolates were greater than 99%. This indicates that the isolates are very closely related and likely originated from a common source. The high genetic diversity among PPV-W strain isolates allowed the identification of potential recombination events between PPV isolates. It appears also that GF 305 peach and Prunus tomentosa are not hosts for the PPV isolate UKR 44189.

The complete nucleotide sequence of a recently discovered Florida (FL) isolate of hibiscus-infecting cilevirus (HiCV) was determined by Sanger sequencing. The movement and coat protein gene sequences of the HiCV-FL isolate are more divergent than other genes of the previously sequenced HiCV-HI (Hawaii) isolate.

The complete genome sequences of three Xanthomonas citri strains isolated from lime trees in Texas were found to belong to the Aw group. All carried nearly identical large plasmids with similarity to those of a citrus canker strain from India and to xanthomonads from Africa and Colombia. All three strains harbored unusual pthA homologs.

The complete genome sequences of three Xanthomonas citri strains isolated from lime trees in Texas were found to belong to the A w group. All carried nearly identical large plasmids with similarity to those of a citrus canker strain from India and to xanthomonads from Africa and Colombia. All three strains harbored unusual pthA homologs.

Plum pox virus (PPV) was identified in Pennsylvania in 1999. The outbreak was limited to a four-county region in southern Pennsylvania. Initial serological and molecular characterization indicated that the isolates in Pennsylvania belong to the D strain of PPV. The Pennsylvania isolates were characterized by sequence analysis, electron microscopy, host range, and vector transmission to determine how these isolates related to their previously studied European counterparts. Genetically, Pennsylvania (PPV-Penn) isolates were more closely related to each other than to any other PPV-D strains, and isolates from the United States, Canada, and Chile were more closely related to each other than to European isolates. The PPV-Penn isolates exist as two clades, suggesting the possibility of multiple introductions. Electron microscopy analysis of PPV-Penn isolates, including cytopathological studies, indicated that the virions were similar to other Potyvirus spp. PPV-Penn isolates had a herbaceous host range similar to that of European D isolates. There were distinct differences in the transmission efficiencies of the two PPV-Penn isolates using Myzus persicae and Aphis spiraecola as vectors; however, both PPV-Penn isolates were transmitted by M. persicae more efficiently than a European D isolate but less efficiently than a European M isolate.

A non-systemic cilevirus producing green ringspot symptoms in ornamental hibiscus (Hibiscus rosa-sinensis), was first reported from Hawaii, USA in 2013, and was named hibiscus infecting Cilevirus (HiCV) (Melzer et al., 2013). The false spider mite Brevipalpus yothersi is associated with symptomatic hibiscus but its role as a vector of HiCV has not yet been demonstrated. Positive sense bi-partite HiCV genome shared 86.2% and 80.0% nucleotide identity with the RNA1 and RNA2 of cytoplasmic citrus leprosis virus -2 (CiLV-C2), respectively (Roy et al., 2013a). Both CiLV-C and -C2 Cileviruses were reported from Colombia but the most prevalent one is CiLV-C2 (Roy et al., 2013a). The 92% amino acid identity between the full genome of these two viruses suggests that HiCV could be a strain of CiLV-C2, but it is not clear if HiCV is capable of infecting and causing symptoms in citrus (Melzer et al., 2013). Recently, we reported natural infection of Hibiscus by CiLV-C2 in Colombia that produced green ring lesions wit...

Hilf, M. E., Mavrodieva, V. A., and Garnsey, S. M. 2005. Genetic marker analysis of a global collection of isolates of Citrus tristeza virus: Characterization and distribution of CTV genotypes and association with symptoms. Phytopathology 95:909-917. Genetic markers amplified from three noncontiguous regions by sequence specific primers designed from the partial or complete genome sequences of Citrus tristeza virus (CTV) isolates T3, T30, T36, and VT were used to assess genetic relatedness of 372 isolates in an international collection. Eighty-five isolates were judged similar to the T3 isolate, 81 to T30, 11 to T36, and 89 to VT. Fifty-one isolates were mixed infections by two or more identifiable viral genotypes, and 55 isolates could not be assigned unequivocally to a group defined by marker patterns. Maximum parsimony analysis of aligned marker sequences supported the grouping of isolates on the basis of marker patterns only. Specific disease symptoms induced in select citrus host plants were shared across molecular groups, although symptoms were least severe among isolates grouped by markers with the T30 isolate and were most severe among isolates grouped by markers with the T3 isolate. Isolates assigned the same genotype showed variable symptoms and symptom severity. A classification strategy for CTV isolates is proposed that combines genetic marker patterns and nucleotide sequence data.

Plum pox, also known as Sharka, is one of the more significant viral diseases of stone fruit trees such as plum, peach, and apricot. It was first reported in Europe in the early 1900s and more recently in Chile in 1992, the United States (Pennsylvania) in 1999, Canada (Ontario and Nova Scotia) in 2000, China in 2001, and Argentina in 2004. Plum pox virus (PPV) was recently detected in two plum (Prunus domestica) trees in an orchard in Niagara County, NY, located within 5 miles from a Canadian plum pox eradication zone. Typical symptoms of chlorotic rings and spots were observed on some of the leaves from these trees. No symptoms were reported prior to the survey collection in July 2006. Survey samples were screened for the presence of PPV by ELISA using the Agdia PPV (Agdia, Elkhart, IN) specific kit that recognizes all strains but C of PPV. Approximately 5% of the survey samples were additionally analyzed by a validated immunocapture reverse transcription (IC-RT)-PCR TaqMan assay in a Cepheid SmartCycler (Cepheid, Sunnyvale, CA). Both replicates of the two New York plum trees produced a positive ELISA reaction in two consecutive tests. The ELISA-positive samples also produced positive results when subjected to the real-time IC-RT-PCR test. The PPV-positive trees were sampled again and an additional 53 samples were collected from trees in the surrounding area. Suspect trees again tested positive, while all the trees in the surrounding area tested negative. The methods used for confirmation included two ELISA tests (Durviz [Valencia, Spain] DAS indirect monoclonal ELISA and Agdia DAS polyclonal ELISA). Confirmatory real-time IC-RT-PCR was performed using universal 3′ nontranslated region (NTR) primers (2,3) in a SYBR Green assay format and a coat protein (CP) primers/probe TaqMan assay (3,4). Further, the New York PPV isolate was identified as PPV D group using a subgroup specific conventional IC-RT-PCR (1). A 1.4-kb sequence fragment from the 3′ end of the New York PPV was sequenced (GenBank Accession No. DG 883816). Comparison of the sequence with the database confirmed this isolate as subgroup D and exhibited a high degree of identity with other PPV D accessions (PPV D Teycheney [Accession No. X16415]; Penn4 [Accession No. DQ465243] Cnd 123-1 [Accession No. AY9553267]; and Cnd 3 [Accession No. AY953262]). To our knowledge, this is the first report of PPV in New York. References: (1) T. Candresse et al. Phytopathology. 88:198, 1998. (2) L. Levy et al. J. Virol. Methods. 49:295, 1994. (3) V. Mavrodieva and L. Levy. Acta Hortic. 657:141, 2004. (4) T. Wetzel et al. J.Virol. Methods 33:355, 1991.