Narcissus Yellow Stripe Virus Research Articles

First report of narcissus yellow stripe virus in Narcissus pseudonarcissus in Korea

First report of narcissus yellow stripe virus in Narcissus pseudonarcissus in Korea

In Silico Virome Analysis of Chinese Narcissus Transcriptomes Reveals Diverse Virus Species and Genetic Diversity at Different Flower Development Stages.

Viromes of Chinese narcissus flowers were explored using transcriptome data from 20 samples collected at different flower development stages. Quality controlled raw data underwent de novo assembly, resulting in 5893 viral contigs that matched the seven virus species. The most abundant viruses were narcissus common latent virus (NCLV), narcissus yellow stripe virus (NYSV), and narcissus mottling-associated virus (NMaV). As flower development stages advanced, white tepal plants showed an increase in the proportion of viral reads, while the variation in viral proportion among yellow tepal plants was relatively small. Narcissus degeneration virus (NDV) dominated the white tepal samples, whereas NDV and NYSV prevailed in the yellow tepal samples. Potyviruses, particularly NDV, are the primary infectious viruses. De novo assembly generated viral contigs for five viruses, yielding complete genomes for NCLV, NDV, narcissus late season yellow virus (NLSYV), and NYSV. Phylogenetic analysis revealed genetic diversity, with distinct NCLV, NMaV, NDV, NLSYV, and NYSV groups. This study provides valuable insights into the viromes and genetic diversity of viruses in Chinese narcissus flowers.

Synonymous Codon Usage Analysis of Three Narcissus Potyviruses.

Narcissus degeneration virus (NDV), narcissus late season yellows virus (NLSYV) and narcissus yellow stripe virus (NYSV), which belong to the genus Potyvirus of the family Potyviridae, cause significant losses in the ornamental value and quality of narcissus. Several previous studies have explored the genetic diversity and evolution rate of narcissus viruses, but the analysis of the synonymous codons of the narcissus viruses is still unclear. Herein, the coat protein (CP) of three viruses is used to analyze the viruses’ phylogeny and codon usage pattern. Phylogenetic analysis showed that NYSV, NDV and NLSYV isolates were divided into five, three and five clusters, respectively, and these clusters seemed to reflect the geographic distribution. The effective number of codon (ENC) values indicated a weak codon usage bias in the CP coding region of the three narcissus viruses. ENC-plot and neutrality analysis showed that the codon usage bias of the three narcissus viruses is all mainly influenced by natural selection compared with the mutation pressure. The three narcissus viruses shared the same best optimal codon (CCA) and the synonymous codon prefers to use codons ending with A/U, compared to C/G. Our study shows the codon analysis of different viruses on the same host for the first time, which indicates the importance of the evolutionary-based design to control these viruses.

Genetic diversity and evolutionary analyses of potyviruses infecting narcissus in Iran.

Potyviruses are among the most important pathogens of dicotyledonous and monocotyledonous ornamentals and crop plants. In this study, leaf samples were collected from symptomatic narcissus plants and weeds in Fars and Tehran provinces of Iran. Enzyme-linked immunosorbent assay using broad-spectrum potyvirus antibodies gave a positive reaction with 38 out of 61 narcissus samples tested (62.3%); the results were confirmed by reverse-transcription polymerase chain reaction using universal NIb primers, and for thirty samples, by sequencing and phylogenetic studies. The results suggested the infection of almost all positive samples with narcissus yellow stripe virus (NYSV); only one sample seemed to be infected with narcissus late season yellows virus (NLSYV). The 3'-end of the genome of the NLSYV isolate and six NYSV isolates, encompassing the complete coat protein gene, was amplified and sequenced using species-specific and universal potyvirus primers. Sequence analysis indicated the presence of NLSYV and NYSV, not previously identified from Western Asia. No evidence of recombination was found in Iranian isolates. Based on phylogenetic analyses, isolates of NLSYV and NYSV clustered into five and three phylogroups, respectively, where all the Iranian isolates fell into distinct subpopulations in groups NLSYV-I and NYSV-II. Multiple sequence alignments showed some phylogroup-specific amino acid substitutions for both viruses. Phylogroup IV and II populations had higher nucleotide diversities as compared with other populations of NLSYV and NYSV, respectively. Our findings revealed the presence of negative selection in the populations of both viruses. Almost no statistically significant gene flow was found between populations of these viruses.Supplementary informationThe online version contains supplementary material available at 10.1007/s42161-021-00985-0.

Three species of Potyvirus genus recorded in ornamental plants, in Brazil

Pepper yellow mosaic virus on Petunia hybrida, bean yellow mosaic virus on Viola odorata and Narcissus yellow stripe virus on Narcissus cyclamineus were identified in Brazil using RT-PCR. Serology, mechanical transmission, host range, and electron microscopy were used to study the viruses further.

Complete genome analysis of a divergent isolate of narcissus yellow stripe virus from China

The complete sequence of ZZ-2, a narcissus yellow stripe virus (NYSV) isolate identified from Chinese narcissus sample in China, was determined. Its entire RNA genomes comprised 9654 nucleotides (nt) in length, excluding the 3′-terminal poly(A) tail and encoded a polyprotein of 3105 amino acids (aa), flanked by 5′ and 3′ untranslated regions (UTR) of 130 and 206 nts, respectively. Sequence analyses indicated that ZZ-2 shared highest 94% nt and 97% aa sequence identities with NYSV NY-CB5 and NY-EH173 isolates at the polyprotein level, whereas only 75% nt and 79% aa identities respectively with the representative of NYSV isolate (NYSV-Zhangzhou), which are less than the threshold values of the proposed species demarcation for the genus Potyvirus. However, ZZ-2 shared more than 81%–97% nt and 83%–99% aa sequence identities with all NYSV isolates in the coat protein, respectively, but less than 80% aa sequences with NLSYV isolates. Phylogenetic analysis revealed that ZZ-2 clustered together with NY-CB5 and NY-EH173. This suggests that ZZ-2, NY-CB5 and NY-EH173 represent a divergent group of NYSV isolates but share specific motifs in the cleavage sites at the junction of P1/HC-Pro and P3/6K1, which are differed from those of NLSYV isolates.

Sequence analyses of RT-PCR products obtained from seven infected leaf samples revealed existence of three potyvirus species in Indian narcissus (Narcissus tazetta L.).

Potyvirus species associated with yellow leaf stripe disease of Indian narcissus (Narcissus tazetta L.) var. Paperwhite has been studied by sequence analyses of ~ 1.5kb genomic fragments obtained from seven RT-PCR amplifications of infected samples. Sequence analysis revealed the occurrence of three potyvirus species: cyrtanthus elatus virus-A (CEVA: KF430815, KF430816, KM066973, KM066974); narcissus yellow stripe virus (NYSV: KM066972, JQ686724) and narcissus degeneration virus (NDV: MK572806). The existence of three potyvirus species: CEVA, NYSV and NDV are being reported in Indian narcissus.

A new potyvirus associated with a mosaic disease of bitter leaf (Vernonia amygdalina) in Nigeria

In a survey of experimental and commercial fields in different locations of southwest Nigeria, severe mosaic, vein banding and yellowing were observed on bitter leaf plants (Vernonia amygdalina). RT-PCR carried out using total RNA isolated from infected leaf samples and a pair of potyvirus-specific primers yielded an amplicon (~700 bp) from all symptomatic samples, indicating the presence of a potyvirus infection. The amplicon was cloned and sequenced. Basic local alignment search tool analysis reveals that while the coat protein (CP) gene was more closely related (77%) to that of narcissus yellow stripe virus (NYSV), the amino acid sequence of the present virus isolate was more closely related (80%) to that of Colombian datura virus (CDV). The phylogenetic analysis of the virus sequences with selected potyvirus sequences revealed the closest relationship with jasmine ringspot virus. Based on sequence identity at the nucleic acid and protein levels as well as on phylogenetic analysis, the isolate in this study was considered not to be an isolate of jasmine ringspot virus. This mosaic disease of Vernonia in Nigeria was induced by a new, hitherto uncharacterized potyvirus, tentatively named Vernonia mosaic virus (VeMV).

A multiplex RT-PCR method for the simultaneous detection of Narcissus yellow stripe virus, Narcissus latent virus and Narcissus mosaic virus

Narcissus (Narcissus spp.) is an important commercial crop and millions of narcissus bulbs are traded across the world annually. Three major viruses, namely, Narcissus yellow stripe virus (NYSV), Narcissus latent virus (NLV) and Narcissus mosaic virus (NMV), have substantial impacts on global crop yields of narcissus. A multiplex RT-PCR assay was developed and used to simultaneously detect these three viruses. Three pairs of virus-specific primers were designed according to the conserved regions of the coat protein (CP) genes, generating expected fragments of 668 bp, 554 bp and 372 bp for NYSV, NLV and NMV, respectively. Specificity and compatibility of primer pairs were tested using uniplex and multiplex RT-PCR. Primer concentration, annealing temperature and cycle number were optimized to enable efficient and balanced amplification of the three viruses. The optimized multiplex RT-PCR was as sensitive as uniplex RT-PCR. Field samples were collected to validate the method, and all the viruses were successfully detected, thereby confirming the effectiveness and reliability of the developed multiplex RT-PCR. This method could be used for large-scale surveys of these three viruses in narcissus and thus might play a role in diagnosis and prevention of these pathogens.

Identification of Narcissus yellow stripe virus and a closely-related potyvirus isolate in plants of Allium carinatum

Identification of <i>Narcissus yellow stripe virus</i> and a closely-related potyvirus isolate in plants of <i>Allium carinatum</i>

The genetic diversity of narcissus viruses related to turnip mosaic virus blur arbitrary boundaries used to discriminate potyvirus species.

Narcissus plants (Narcissus tazetta var. chinensis) showing mosaic or striping leaves were collected from around Japan, and tested for virus infections using potyvirus-specific primers. Many were found to be infected with a macluravirus and mixtures of different potyviruses, one third of them narcissus yellow stripe virus (NYSV)-like viruses. Genomes of nine of the NYSV-like viruses were sequenced and, together with four already published, provided data for phylogenetic and pairwise identity analyses of their place in the turnip mosaic virus (TuMV) phylogenetic group. Using existing ICTV criteria for defining potyvirus species, the narcissus viruses in TuMV group were found to be from five species; the previously described NLSYV, and four new species we call narcissus virus 1 (NV-1) and narcissus yellow stripe-1 to -3 (NYSV-1, NYSV-2 and NYSV-3). However, as all are from a single host species, and natural recombinants with NV-1 and NYSV-3 'parents have been found in China and India, we also conclude that they could be considered to be members of a single mega-species, narcissus virus; the criteria for defining such a potyvirus species would then be that their polyprotein sequences have greater than 69% identical nucleotides and greater than 75% identical amino acids.

Evolutionary rates and genetic diversities of mixed potyviruses in Narcissus

There is no attempt to evaluate evolutionary rates, timescales and diversities of viruses collected from mixedly infected hosts in nature. Plants of the genus Narcissus are a monocotyledon and are susceptible to several viruses. In this study, narcissus plants (Narcissus tazetta var. chinensis) showing mosaic or striping leaves were collected in Japan, and these were investigated for potyvirus infections using potyvirus-specific primers. Individual narcissus plants were found frequently to be mixedly infected with different potyviruses, different isolates and quasispecies of same virus. The viruses were potyviruses and a macluravirus in the family Potyviridae, namely Narcissus late season yellows virus (NLSYV), Narcissus yellow stripe virus (NYSV), Narcissus degeneration virus (NDV), Cyrtanthus elatus virus A (CyEVA) and Narcissus latent virus (NLV). Genetic diversities of coat protein coding region of different virus species were different; NYSV and CyEVA were most diverse whereas NDV was least. Evolutionary rates of all five narcissus viruses were 1.33–7.15×10−3nt/site/year and were similar. The most recent common ancestors (TMRCAs) varied between virus species; NYSV and CyEVA were the oldest whereas NDV was the youngest. Thus, the oldness of TMRCAs of the viruses correlated well with the greatness of nucleotide diversities.

Complete genome analysis of three isolates of narcissus late season yellows virus and two of narcissus yellow stripe virus: three species or one?

Complete genome sequences of two new isolates of narcissus late season yellows virus (NLSYV) from Australia were compared with the other NLSYV genome from China and with two complete genomes of isolates designated narcissus yellow stripe virus (NYSV), one from Australia and the other from China. On the basis of symptoms on natural and experimental host species, and genome sequence identity, the isolates could either be classified as closely related members of three different species or placed together in one taxon. Options for classification of these potyvirus isolates are discussed.

Complete genome sequence of narcissus late season yellows virus infecting Chinese narcissus in China

The complete genome sequence of a Chinese narcissus isolate of narcissus late season yellows virus from Zhangzhou, China (NLSYV-ZZ), was determined to be 9,651 nucleotides in length, excluding the 3'-terminal poly (A) tail, by amplification and sequencing of virus RNA. The viral genome contains a single long open reading frame of 9,315 nucleotides encoding a polyprotein of 3,105 amino acids. The polyprotein was predicted to be cleaved into ten mature proteins by three viral proteases. Complete genome sequence comparison and phylogenetic analysis indicated that NLSYV-ZZ was most closely related to narcissus yellow stripe virus (NYSV), which was also isolated from narcissus. These viruses shared 69.9 % identity in their complete nucleotide sequences and 77.0 % identity in their polyprotein amino acid sequences.

Complete genome sequences of seven carlavirus and potyvirus isolates from Narcissus and Hippeastrum plants in Australia, and proposals to clarify their naming

Complete genome sequences were obtained from two isolates of the carlavirus nerine latent virus from hippeastrum and narcissus plants, two isolates of the potyvirus hippeastrum mosaic virus from a hippeastrum plant, and one isolate each of the potyviruses narcissus degeneration virus, narcissus yellow stripe virus and Vallota speciosa virus from narcissus plants. Proposals are made to clarify the current confusion surrounding the naming of some of these viruses.

Determination of the complete nucleotide sequence of a lupine potyvirus isolate from the Czech Republic reveals that it belongs to a new member of the genus Potyvirus

The complete nucleotide sequence of the ssRNA genome of a lupine potyvirus (LP) isolate was determined. It comprised 10,113 nucleotides excluding the poly(A) tail. Phylogenetic analysis of CP protein sequences identified pepper veinal mottle virus, narcissus yellow stripe virus, and chili veinal mottle virus as the closest relatives, sharing coat protein amino acid sequence identities of only about 64% with the LP isolate. Thus, LP can be regarded as a member of a newly described potyvirus species, for which the name Lupine mosaic virus (LuMV) is proposed.

First Report of Narcissus degeneration virus, Narcissus late season yellows virus, and Narcissus symptomless virus on Narcissus in New Zealand

In September 2008, Narcissus plants originating from commercial nurseries in Taranaki (TK) in New Zealand's North Island and Canterbury (CB) in the South Island were received showing leaf mottling, flower distortion, and color break. The CB plant also showed stunting. Filamentous virus particles (700 to 900 nm long) were seen in crude sap of both plants with a transmission electron microscope. Total RNA was isolated from the leaves of both plants with an RNeasy Plant Mini Kit (Qiagen, Chatsworth, CA), and cDNA was synthesized by Superscript III (Invitrogen, Carlsbad, CA). cDNA was used in PCR to test for viruses in the following genera: Allexivirus, Carlavirus, Cucumovirus, Nepovirus A and B, Potyvirus, Potexvirus, Tospovirus, and Tobravirus. Both plants tested positive for potyvirus using generic potyvirus primers (3). Amplicons from both plants were directly sequenced. The forward and reverse sequence from the CB plant matched sequences in the GenBank database for Narcissus late season yellows virus (NLSYV) and Narcissus degeneration virus (NDV), respectively. The potyvirus amplicon from the CB plant was cloned and sequenced. Sequence from independent clones was obtained for NLYSV only (No. FJ546721), and this sequence showed 97% nucleotide identity to NLYSV No. EU887015. The CB plant was tested with a second set of generic potyvirus primers using forward (PV1SP6) (2) and reverse primers (U335) (1). BLASTN analysis of the sequence obtained from independent clones (No. FJ543718) matched sequence for NDV only (97% nucleotide identity to No. AM182028). BLASTN analysis of the potyvirus obtained for the TK plant (No. FJ546720) showed 97% nucleotide identity to NLSYV (No. EU887015). The TK plant also tested positive for a carlavirus using commercial primers (Agdia, Elkhart, IN) and unpublished generic carlavirus primers (A. Blowers, personal communication). Amplicons from both PCRs were cloned and sequenced. BLASTN analysis of both sequences (Nos. FJ546719 and GQ205442) showed 94% nucleotide identity to Narcissus symptomless virus (NSV) No. AM182569. Both plants were also tested for NLSYV, Narcissus virus Q, Narcissus latent virus, and Narcissus yellow stripe virus by indirect ELISA (Neogen, Lansing, MI). Results confirmed the presence of NLSYV in both plants but the plants were negative for the other viruses. NLSYV has been detected previously from Narcissus pseudonarcissus L. (daffodil) (D. Hunter, personal communication); however, to our knowledge, this is the first official report of NDV, NLSYV, and NSV in New Zealand. Since both plants tested negative for several other viruses by PCR and ELISA, this would suggest that the symptoms observed may have been caused by NSV, NLSYV, NDV, or as a result of a mixed infection. However, symptoms were not confirmed using Koch's postulate. NSV has been reported in the literature as symptomless. NLYSV has been reported to be a possible cause of leaf chlorosis and striping and NDV has been associated with chlorotic leaf striping in N. tazetta plants (4). Since Narcissus is an important flower crop for domestic production in New Zealand, the reduction in flower quality observed when these viruses are present may be of economic significance in commercial nurseries.

Identification of a potyvirus associated with mosaic disease of Narcissus sp. in India

Narcissus tazetta cv. Paperwhite is an important ornamental for the floriculture industry. Narcissus is susceptible to three members of genus Potyvirus, namely Narcissus yellow stripe virus, Narcissus late season yellows virus and Narcissus degeneration virus, plus Narcissus latent virus (genus Macluravirus, family Potyviridae). A disease characterized by severe mosaic and light green to yellow leaf stripes, was observed on Narcissus in an experimental plot at the National Botanical Research Institute, Lucknow. Affected plants also showed extreme reduction in their growth, and loss of yield and bloom quality. Total RNA was extracted from 100 mg of leaf tissue as described by Gibbs & MacKenzie (1997). RT-PCR was performed with potyvirid specific primers Pot1 and Pot2 (Gibbs & MacKenzie, 1997) to amplify part of the NIb gene, the coat protein (CP) gene and the 3′ untranslated region (UTR). The amplified DNA fragment of c. 1·5 kb was cloned into the p-drive cloning vector (QIAGEN) and sequenced (GenBank accession DQ991145). The CP gene nucleotide sequence showed 98% identity with Chinese narcissus potyvirus Chongming isolate (AJ311374·1), 97% with Chinese narcissus potyvirus Zhangzhou isolate (AJ311373·1) and 95% with Lycorsis potyvirus (AF511486·1). The 3′-UTR (148 nt.) shared 100% identity with the Chinese narcissus Chongming and Zhangzhou isolates and 97% identity with Lycoris potyvirus (AF511486·1). Earlier investigations in India (Aminuddin et al., 1989, 1999), based mainly on biological, serological and electron microscopic properties demonstrated the association of an unidentified potyvirus with severe mosaic disease of Narcissus tazetta. However, nucleotide sequence information (CP gene and 3′ UTR) available in this study clearly established the identity of the associated potyvirus, at the species level, as the virus first recorded as Lycoris potyvirus. This is the first specific identification of a potyvirus from narcissus in India. However, Narcissus spp. are prone to mixed viral infections (Chen et al., 2003) so this potyvirus may not be the sole agent causing the mosaic disease.

Complete nucleotide sequence of the genomic RNA of Narcissus yellow stripe virus from Chinese narcissus in Zhangzhou city, China

Complete nucleotide sequence of the genomic RNA of Narcissus yellow stripe virus from Chinese narcissus in Zhangzhou city, China

Molecular Characterization of Carla‐ and Potyviruses from Narcissus in China

AbstractConserved carlavirus and potyvirus primers were used in reverse transcriptase‐polymerase chain reaction (RT‐PCR) to amplify virus fragments from Chinese narcissus (Narcissus tazetta var. chinensis) in China and the fragments were subsequently sequenced and compared in phylogenetic analyses. Samples from Fujiang province and Shanghai contained either one or two potyviruses and a carlavirus. One potyvirus (PY1) showed a distant relationship to Iris severe mosaic virus, Onion yellow dwarf virus and Shallot yellow stripe virus, while the other (only in the Fujiang sample, PY2) was most closely related to Turnip mosaic virus (TuMV). Similar experiments using glasshouse grown Narcissus originating from the UK contained Ornithogalum mosaic virus and another potyvirus (PY3) in the TuMV/PY2 cluster. Comparisons with previously determined sequence fragments indicated that PY2 was probably Narcissus yellow stripe virus and PY3 Narcissus late season yellow virus. Carlavirus fragments from both Chinese sites seemed to be of the same virus, which was most closely related in phylogenetic analyses to Potato virus M, Aconitum latent virus and Hop latent virus. It is most probably a new member of the genus Carlavirus and has been tentatively named Narcissus common latent virus.