Development and Application of a Duplex RT-RPA Assay for the Simultaneous Detection of Cymbidium mosaic virus and Odontoglossum ringspot virus.

Cymbidium mosaic virus (CymMV) and Odontoglossum ringspot virus (ORSV) are among the world's most serious and widespread orchid viruses; they often infect orchids, causing devastating losses to the orchid industry. Therefore, it is critical to establish a method that can rapidly and accurately detect viruses in the field using simple instruments, which will largely reduce the further spread of viruses and improve the quality of the orchid industry and is suitable for mass promotion and application at grassroots agrotechnical service points. In this investigation, we established a rapid amplification method for virus detection at 39 °C for 35 min to detect the presence of CymMV and ORSV simultaneously, sensitively, and specifically in orchids. Primers for the capsid protein (CP)-encoding genes of both viruses were designed and screened, and the reaction conditions were optimized. The experimental amplification process was completed in just 35 min at 39 °C. There were no instances of nonspecific amplification observed when nine other viruses were present. The RPA approach had detection limits of 104 and 103 copies for pMD19T-CymMV and pMD19T-ORSV, respectively. Moreover, the duplex RT-RPA investigation confirmed sensitivity and accuracy via a comparison of detection results from 20 field samples with those of a gene chip. This study presents a precise and reliable detection method for CymMV and ORSV using RT-RPA. The results demonstrate the potential of this method for rapid virus detection. It is evident that this method could have practical applications in virus detection processes.

Early-Stage Phenotyping of Sweet Potato Virus Disease Caused by Sweet Potato Chlorotic Stunt Virus and Sweet Potato Virus C to Support Breeding.

Sweet potato virus disease (SPVD) is a global constraint to sweetpotato (Ipomoea batatas) production, especially under intensive cultivation in the humid tropics such as East Africa. The objectives of this study were to develop a precision SPVD phenotyping protocol, to find new SPVD-resistant genotypes, and to standardize the first stages of screening for SPVD resistance. The first part of the protocol was based on enzyme-linked immunosorbent assay results for sweet potato chlorotic stunt virus (SPCSV) and sweet potato virus C (SPVC) with adjustments to a negative control (uninfected clone Tanzania) and was performed on a prebreeding population (VZ08) comprising 455 clones and 27 check clones graft inoculated under screenhouse conditions. The second part included field studies with 52 selected clones for SPCSV resistance from VZ08 and 8 checks. In screenhouse conditions, the resistant and susceptible check clones performed as expected; 63 clones from VZ08 exhibited lower relative absorbance values for SPCSV and SPVC than inoculated check Tanzania. Field experiments confirmed SPVD resistance of several clones selected by relative absorbance values (nine resistant clones in two locations; that is, 17.3% of the screenhouse selection), supporting the reliability of our method for SPVD-resistance selection. Two clones were promising, exhibiting high storage root yields of 28.7 to 34.9 t ha-1 and SPVD resistance, based on the proposed selection procedure. This modified serological analysis for SPVD-resistance phenotyping might lead to more efficient development of resistant varieties by reducing costs and time at early stages, and provide solid data for marker-assisted selection with a quantitative tool for classifying resistance.[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Phylogenetics and Evolution of Potato Virus V: Another Potyvirus that Originated in the Andes.

Potato virus V (PVV) causes a disease of potato (Solanum tubersosum) in South and Central America, Europe, and the Middle East. We report here the complete genomic sequences of 42 new PVV isolates from the potato's Andean domestication center in Peru and of eight historical or recent isolates from Europe. When the principal open reading frames of these genomic sequences together with those of nine previously published genomic sequences were analyzed, only two from Peru and one from Iran were found to be recombinant. The phylogeny of the 56 nonrecombinant open reading frame sequences showed that the PVV population had two major phylogroups, one of which formed three minor phylogroups (A1 to A3) of isolates, all of which are found only in the Andean region of South America (Peru and Colombia), and the other formed two minor phylogroups, a basal one of Andean isolates (A4) that is paraphyletic to a crown cluster containing all the isolates found outside South America (World). This suggests that PVV originated in the Andean region, with only one minor phylogroup spreading elsewhere in the world. In minor phylogroups A1 and A3, there were two subclades on long branches containing isolates from S. phureja evolving more rapidly than the others, and these interfered with dating calculations. Although no temporal signal was directly detected among the dated nonrecombinant sequences, PVV and potato virus Y (PVY) are from the same potyvirus lineage and are ecologically similar, so "subtree dating" was done via a single maximum likelihood phylogeny of PVV and PVY sequences, and PVY's well-supported 157 ce "time to most common recent ancestor" was extrapolated to date that of PVV as 29 bce. Thus the independent historical coincidences supporting the datings of the PVV and PVY phylogenies are the same; PVV arose ≥2,000 years ago in the Andes and was taken to Europe during the Columbian Exchange, where it diversified around 1853 ce, soon after the European potato late blight pandemic. PVV is likely to be more widespread than currently realized and is of biosecurity relevance for world regions that have not yet recorded its presence.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Proteolytic Processing of Plant Proteins by Potyvirus NIa Proteases.

The NIa protease of potyviruses is a chymotrypsin-like cysteine protease related to the picornavirus 3C protease. It is also a multifunctional protein known to play multiple roles during virus infection. Picornavirus 3C proteases cleave hundreds of host proteins to facilitate virus infection. However, whether or not potyvirus NIa proteases cleave plant proteins has so far not been tested. Regular expression search using the cleavage site consensus sequence [EQN]xVxH[QE]/[SGTA] for the plum pox virus (PPV) protease identified 90 to 94 putative cleavage events in the proteomes of Prunus persica (a crop severely affected by PPV), Arabidopsis thaliana, and Nicotiana benthamiana (two experimental hosts). In vitro processing assays confirmed cleavage of six A. thaliana and five P. persica proteins by the PPV protease. These proteins were also cleaved in vitro by the protease of turnip mosaic virus (TuMV), which has a similar specificity. We confirmed in vivo cleavage of a transiently expressed tagged version of AtEML2, an EMSY-like protein belonging to a family of nuclear histone readers known to be involved in pathogen resistance. Cleavage of AtEML2 was efficient and was observed in plants that coexpressed the PPV or TuMV NIa proteases or in plants that were infected with TuMV. We also showed partial in vivo cleavage of AtDUF707, a membrane protein annotated as lysine ketoglutarate reductase trans-splicing protein. Although cleavage of the corresponding endogenous plant proteins remains to be confirmed, the results show that a plant virus protease can cleave host proteins during virus infection and highlight a new layer of plant-virus interactions. IMPORTANCE Viruses are highly adaptive and use multiple molecular mechanisms to highjack or modify the cellular resources to their advantage. They must also counteract or evade host defense responses. One well-characterized mechanism used by vertebrate viruses is the proteolytic cleavage of host proteins to inhibit the activities of these proteins and/or to produce cleaved protein fragments that are beneficial to the virus infection cycle. Even though almost half of the known plant viruses encode at least one protease, it was not known whether plant viruses employ this strategy. Using an in silico prediction approach and the well-characterized specificity of potyvirus NIa proteases, we were able to identify hundreds of putative cleavage sites in plant proteins, several of which were validated by downstream experiments. It can be anticipated that many other plant virus proteases also cleave host proteins and that the identification of these cleavage events will lead to novel antiviral strategies.

Coinfection of Cotton Plants with Watermelon Mosaic Virus and a Novel Polerovirus in China.

Cotton is the most important fiber crop worldwide. To determine the presence of viruses in cotton plants showing leaf roll and vein yellowing symptoms in Henan Province of China, a small RNA-based deep sequencing approach was performed. Analysis of the de novo-assembled contigs followed by reverse transcription PCR allowed the reconstruction of watermelon mosaic virus and an unknown virus. The genome of the unknown virus was determined to be 5870 nucleotides in length, and has a genomic organization with characteristic features of previously reported poleroviruses. Sequence analysis revealed that the virus was closely related to, but significantly different from, cotton leafroll dwarf virus, a polerovirus of the family Solemoviridae. This virus had less than 90% amino acid sequence identity in the products of both ORF0 and ORF1. According to the polerovirus species demarcation criteria set by the International Committee on Taxonomy of Viruses, this virus should be assigned to a new polerovirus species, for which we propose the name "cotton leaf roll virus".

Complete genome sequence and genome organization of scorzonera virus A (SCoVA), a novel member of the genus Potyvirus.

The complete genomic sequence of scorzonera virus A (SCoVA) from a Scorzonera austriaca Willd. plant in South Korea was determined by high-throughput sequencing and confirmed by Sanger sequencing. The SCoVA genome contains 9867 nucleotides, excluding the 3'-terminal poly(A) tail. The SCoVA genome structure is typical of potyviruses and contains a single open reading frame encoding a large putative polyprotein of 3168 amino acids. Pairwise comparison analysis of the complete genome and polyprotein sequences of SCoVA with those of other potyviruses showed that they shared the highest nucleotide and amino acid sequences identity (54.47% and 49.57%, respectively) with those of lettuce mosaic virus (GenBank accession number KJ161185). Phylogenetic analysis of the amino acid sequence of the polyprotein confirmed that SCoVA belongs to the genus Potyvirus. These findings suggest that SCoVA should be considered a novel member of the genus Potyvirus, family Potyviridae.

Metagenomic Analysis of Marigold: Mixed Infection Including Two New Viruses.

Marigold plants with symptoms of mosaic, crinkle, leaf curl and necrosis were observed and small RNA and ribo-depleted total RNA deep sequencing were conducted to identify the associated viruses. Broad bean wilt virus 2, cucumber mosaic virus, turnip mosaic virus, a new potyvirus tentatively named marigold mosaic virus (MMV) and a new partitivirus named as marigold cryptic virus (MCV) were finally identified. Complete genome sequence analysis showed MMV was 9811 nt in length, encoding a large polyprotein with highest aa sequence identity (57%) with the putative potyvirus polygonatumkingianum virus 1. Phylogenetic analysis with the definite potyviruses based on the polyprotein sequence showed MMV clustered closest to plum pox virus. The complete genome of MCV comprised of dsRNA1 (1583 bp) and dsRNA2 (1459 bp), encoding the RNA-dependent RNA polymerase (RdRp), and coat protein (CP), respectively. MCV RdRp shared the highest (75.7%) aa sequence identity with the unclassified partitivirus ambrosia cryptic virus 2, and 59.0%, 57.1%, 56.1%, 54.5% and 33.7% with the corresponding region of the definite delta-partitiviruses, pepper cryptic virus 2, beet cryptic virus 3, beet cryptic virus 2, pepper cryptic virus 1 and fig cryptic virus, respectively. Phylogenetic analysis based on the RdRp aa sequence showed MCV clustered into the delta-partitivirus group. These findings enriched our knowledge of viruses infecting marigold, but the association of the observed symptom and the identified viruses and the biological characterization of the new viruses should be further investigated.

Complete genome sequences of anemone mosaic virus and ranunculus mild mosaic virus isolated from anemone imported from the Netherlands into Japan.

Anemone mosaic virus (AnMV) and ranunculus mild mosaic virus (RanMMV) infect anemone plants, which exhibit characteristic mosaic patterns on their leaves. Employing next-generation sequencing of plant material imported from the Netherlands, the complete genome sequences of these two viruses were determined for the first time. AnMV and RanMMV have 9698 and 9537 nucleotides (nt), respectively, excluding the poly(A) tail. They share 80.0%/82.0% and 98.0%/97.0% nt/amino acid (aa) sequence identity, which is above the species demarcation value, in the previously reported AnMV and RanMMV coat protein sequences, but they share 69.0%/70.0% nt/aa sequence identity or less with other potyviruses in all 10 mature protein coding regions of the genome. Additionally, phylogenetic analysis confirmed the relationship of the AnMV and RanMMV genome sequences to previously reported partial sequences and placed them within the genus Potyvirus. These results show that these two viruses represent separate species within the genus Potyvirus.

Analysis of the molecular and biological variability of Zucchini yellow mosaic virus isolates from Iran and Iraq.

During the growing season of 2018, several field-grown cucurbit plants in different parts of Iraq and Iran were surveyed for the presence of zucchini yellow mosaic virus (ZYMV), using two degenerate primer pairs (CIF/Rev and NIb2F/3R) targeting the two separated partial regions of the potyvirus genome (CI and NIb respectively). 7 out of 20 samples were confirmed to be infected with ZYMV. Phylogenetic analyses based on the CI gene grouped all Iranian and two Iraqi (ZYMV1 and ZYMV2) isolates together with isolates from the Middle East in the subgroup (AI), whereas the other Iraqi (ZYMV3 and ZYMV4) isolates were clustered in the subgroup (DI), which was only consisted of American isolates. The highest and lowest identity between the studied isolates and the GenBank isolates showed that the two genes (CI, NIb) of each isolate particularly the Iraqi isolates were more similar to a specific and geographically scattered mosaic of worldwide isolates, suggestive of mixed infection might have occurred between different worldwide isolates in Iraq. Furthermore, the first complete nucleotide sequence of an Iraqi ZYMV (ZYMV-Iq) isolate was done, using the Illumina sequencing technique. The complete nucleotide sequence of ZYMV-Iq isolate was 9650 nt, excluding the 3'poly (A) tail. ZYMV-Iq isolate shared the highest nt identity of 98.8% with an American (KC665630) isolate. Phylogenetic analysis based on the full genome sequence placed ZYMV-Iq in subgroup A of group I alongside 18 isolates from the US and two isolates from Australia. In addition, recombination analysis detected lone significant recombination between ZYMV-Iq and South Korean (AY279000) isolate. Moreover, the results showed that symptom intensity was varied across experimental host plants.

Three Strains of Tobacco etch virus Distinctly Alter the Transcriptome of Apical Stem Tissue in Capsicum annuum during Infection.

Tobacco etch virus (TEV; genus Potyvirus) is flexuous rod shaped with a single molecule of single-stranded RNA and causes serious yield losses in species in the Solanaceae. Three TEV strains (HAT, Mex21, and N) are genetically distinct and cause different disease symptoms in plants. Here, a transcriptomic RNA sequencing approach was taken for each TEV strain to evaluate gene expression of the apical stem segment of pepper plants during two stages of disease development. Distinct profiles of Differentially Expressed Genes (DEGs) were identified for each TEV strain. DEG numbers increased with degree of symptom severity: 24 from HAT, 1190 from Mex21, and 4010 from N. At 7 days post-inoculation (dpi), when systemic symptoms were similar, there were few DEGs for HAT- and Mex21-infected plants, whereas N-infected plants had 2516 DEGs. DEG patterns from 7 to 14 dpi corresponded to severity of disease symptoms: milder disease with smaller DEG changes for HAT and Mex21 and severe disease with larger DEG changes for N. Strikingly, in each of these comparisons, there are very few overlapping DEGs among the TEV strains, including no overlapping DEGs between all three strains at 7 or 14 dpi.

Emerging strains of watermelon mosaic virus in Southeastern France: model-based estimation of the dates and places of introduction.

Where and when alien organisms are successfully introduced are central questions to elucidate biotic and abiotic conditions favorable to the introduction, establishment and spread of invasive species. We propose a modelling framework to analyze multiple introductions by several invasive genotypes or genetic variants, in competition with a resident population, when observations provide knowledge on the relative proportions of each variant at some dates and places. This framework is based on a mechanistic-statistical model coupling a reaction-diffusion model with a probabilistic observation model. We apply it to a spatio-temporal dataset reporting the relative proportions of five genetic variants of watermelon mosaic virus (WMV, genus Potyvirus, family Potyviridae) in infections of commercial cucurbit fields. Despite the parsimonious nature of the model, it succeeds in fitting the data well and provides an estimation of the dates and places of successful introduction of each emerging variant as well as a reconstruction of the dynamics of each variant since its introduction.

Different potato virus Y strains frequently co-localize in single epidermal leaf cells and in the aphid stylet.

Single aphids can simultaneously or sequentially acquire and transmit multiple potato virus Y (PVY) strains. Multiple PVY strains are often found in the same field and occasionally within the same plant, but little is known about how PVY strains interact in plants or in aphid stylets. Immuno-staining and confocal microscopy were used to examine the spatial and temporal dynamics of PVY strain mixtures (PVYO and PVYNTN or PVYO and PVYN) in epidermal leaf cells of 'Samsun NN' tobacco and 'Goldrush' potato. Virus binding and localization was also examined in aphid stylets following acquisition. Both strains systemically infected tobacco and co-localized in cells of all leaves examined; however, the relative amounts of each virus changed over time. Early in the tobacco infection, when mosaic symptoms were observed, PVYO dominated the infection although PVYNTN was detected in some cells. As the infection progressed and vein necrosis developed, PVYNTN was prevalent. Co-localization of PVYO and PVYN was also observed in epidermal cells of potato leaves with most cells infected with both viruses. Furthermore, two strains could be detected binding to the distal end of aphid stylets following virus acquisition from a plant infected with a strain mixture. These data are in contrast with the traditional belief of spatial separation of two closely related potyviruses and suggest apparent non-antagonistic interaction between PVY strains that could help explain the multitude of emerging recombinant PVY strains discovered in potato in recent years.

Genomic analysis of the brassica pathogen turnip mosaic potyvirus reveals its spread along the former trade routes of the Silk Road.

Plant pathogens have agricultural impacts on a global scale and resolving the timing and route of their spread can aid crop protection and inform control strategies. However, the evolutionary and phylogeographic history of plant pathogens in Eurasia remains largely unknown because of the difficulties in sampling across such a large landmass. Here, we show that turnip mosaic potyvirus (TuMV), a significant pathogen of brassica crops, spread from west to east across Eurasia from about the 17th century CE. We used a Bayesian phylogenetic approach to analyze 579 whole genome sequences and up to 713 partial sequences of TuMV, including 122 previously unknown genome sequences from isolates that we collected over the past five decades. Our phylogeographic and molecular clock analyses showed that TuMV isolates of the Asian-Brassica/Raphanus (BR) and basal-BR groups and world-Brassica3 (B3) subgroup spread from the center of emergence to the rest of Eurasia in relation to the host plants grown in each country. The migration pathways of TuMV have retraced some of the major historical trade arteries in Eurasia, a network that formed the Silk Road, and the regional variation of the virus is partly characterized by different type patterns of recombinants. Our study presents a complex and detailed picture of the timescale and major transmission routes of an important plant pathogen.

Complete genome sequence of passiflora virus Y infecting passion fruit in China.

The complete genome sequence of passiflora virus Y (PaVY) from passion fruit growing in Guangdong province, China, was determined. The entire positive single-strand RNA genome comprises 9681 nucleotides (nt) excluding the poly(A) tail and encodes a polyprotein of 3084 amino acids flanked by 5' and 3' untranslated regions of 169 and 257 nt, respectively. In sequence comparisons and phylogenetic analysis, PaVY appears to represent a new species in the bean common mosaic virus subgroup of the genus Potyvirus. This is the first report of the complete genome sequence of PaVY and the first report of this virus in China.

Complete genome sequence of ornithogalum virus 3.

Ornithogalum thyrsoides, a widely cultivated bulbous ornamental plant endemic to South Africa, has significant commercial value as a pot plant and for the production of cut flowers. However, infection by viruses threatens the success of commercial cultivation, as symptoms negatively affect the appearance of the plant and flowers. To date, four Ornithogalum-infecting viruses have been reported. Complete genome sequence data are available for three of these viruses, but the genome of the potyvirus ornithogalum virus 3 (OV3) has not been fully sequenced. In this study, the complete sequence of OV3 was determined by high-throughput sequencing (HTS) and validated by Sanger sequencing. Based on recognition of protease cleavage patterns and multiple sequence alignments with closely related viruses, the polyprotein of OV3 was predicted to be proteolytically cleaved to produce 10 mature peptides containing domains conserved in members of the genus Potyvirus. Phylogenetic analysis and species demarcation criteria confirm the previous classification of OV3 as a member of a separate species in this genus. This is the first report of a complete genome sequence of OV3.

Potato Virus Y Emergence and Evolution from the Andes of South America to Become a Major Destructive Pathogen of Potato and Other Solanaceous Crops Worldwide.

The potato was introduced to Europe from the Andes of South America in the 16th century, and today it is grown worldwide; it is a nutritious staple food eaten by millions and underpins food security in many countries. Unknowingly, potato virus Y (PVY) was also introduced through trade in infected potato tubers, and it has become the most important viral pathogen of potato. Phylogenetic analysis has revealed the spread and emergence of strains of PVY, including strains causing economically important diseases in tobacco, tomato and pepper, and that the virus continues to evolve with the relatively recent emergence of new damaging recombinant strains. High-throughput, next-generation sequencing platforms provide powerful tools for detection, identification and surveillance of new PVY strains. Aphid vectors of PVY are expected to increase in incidence and abundance in a warmer climate, which will increase the risk of virus spread. Wider deployment of crop cultivars carrying virus resistance will be an important means of defence against infection. New cutting-edge biotechnological tools such as CRISPR and SIGS offer a means for rapid engineering of resistance in established cultivars. We conclude that in future, human activities and ingenuity should be brought to bear to control PVY and the emergence of new strains in key crops by increased focus on host resistance and factors driving virus evolution and spread.

Identification and full genomic sequence of nerine yellow stripe virus.

This study reports the first complete genome sequence of nerine yellow stripe virus (NeYSV, GenBank MT396083). The genome consists of 10,165 nucleotides, excluding the 3'-terminal poly(A) tail. A single open reading frame encodes a large polyprotein of 3294 amino acids with typical potyvirus features. The nuclear inclusion b and coat protein region shares 95% identity with a previously reported partial NeYSV sequence (NC_043153.1). Phylogenetic analysis of the polyprotein amino acid sequence showed that NeYSV clustered with hippeastrum mosaic virus (HiMV YP_006382256.1).

Small RNA profiling analysis of two recombinant strains of potato virus Y in infected tobacco plants.

Plant viral infections lead to accumulation of virus-derived small interfering RNAs (vsiRNAs) as a result of host defense mechanisms. High-throughput sequencing technology enables vsiRNA profiling analyses from virus infected plants, which provide important insights into virus-host interactions. Potato virus Y (PVY) is a detrimental plant pathogen that can infect a variety of solanaceous crops, e.g., potato, tobacco, tomato, and pepper. We analyzed and characterized vsiRNAs derived from Nicotiana tabacum cv. Samsun infected with two recombinant PVY strains, N-Wi and NTN. We observed that the average percentage of vsiRNAs derived from plants infected with N-Wi was higher than from plants infected with NTN, indicating that N-Wi invokes a stronger host response than NTN in tobacco. The size distribution pattern and polarity of vsiRNAs were similar between both virus strains with the 21 and 22 nucleotide (nt) vsiRNA classes as most predominant and the sense/antisense vsiRNAs ratio nearly equal in the 20-24 nt class. However, the percentage of sense vsiRNAs was significantly higher in the 25-26 nt long vsiRNAs. Distinct vsiRNA hotspots, identifying highly abundant reads of different unique vsiRNA sequences, were observed in both viral genomes. Previous studies found an A or U bias at the 5' terminal nucleotide position of 21 nt vsiRNAs; in contrast, our analysis revealed a C and U nucleotide bias. This study provides insights that will help further elucidate differential processing of vsiRNAs in plant antiviral defense.

Complete genome sequence of a novel potyvirus isolated from Polygonatum kingianum.

The complete genome sequence of a putative novel potyvirus, tentatively named "Polygonatum kingianum virus 1" (PKgV1), infecting Polygonatum kingianum in China was determined (GenBank accession no. MK427056). PKgV1 has a genome organization that is typical of potyviruses, with a single large open reading frame (nt 123-9236) that encodes a 3037-aa polyprotein that is predicted to be cleaved into 10 mature proteins by virus-encoded proteases. Nine cleavage sites and several conserved motifs were identified in PKgV1 by comparative sequence analysis. Pairwise comparisons revealed that the PKgV1 polyprotein shares 52.0-56.2% nucleotide and 49.2-52.8% amino acid sequence identity with members of the genus Potyvirus. Phylogenetic analysis indicated that PKgV1 clustered with members of the genus Potyvirus and that it is closely related to but distinct from lettuce mosaic virus (LMV, accession no. KJ161186). These results suggest that Polygonatum kingianum virus 1 (PKgV1) is a new member of the genus Potyvirus of the family Potyviridae.

Analysis of codon usage bias in potato virus Y non-recombinant strains.

Potato virus Y (PVY) is a member of the genus Potyvirus, family Potyviridae, is considered one of the most devastating pest affecting economically important crops, such as potato, tobacco, tomato and pepper, representing a serious threat due to high incidence and worldwide distribution. Its economic significance as well as it biological and molecular complexities have aroused great attention, thus several studies have explore it genetic characteristics. However, little is known about PVY codon usage. To shed light on the relation of codon usage among viruses and their hosts is extremely important to understand virus survival, fitness and evolution. In this study, we performed a comprehensive analysis of codon usage and composition of PVY non-recombinant strains (PVYN-NA, PVYEu-N, PVYO, PVYO5, PVYC) based on 130 complete open reading frame sequences extracted from public databases. Furthermore, similarities between the synonymous codon usage of PVY and its main hosts were investigated. The results obtained in the current study suggest that the overall codon usage among PVY genotypes is similar and slightly biased. PVY codon usage is strongly influenced by mutational bias, but also by G + C compositional constraint and dinucleotide composition. Furthermore, similarities among codon usage preferences between PVY strains and analyzed hosts were observed.