Molecular aspects of potato virus Y transmission by aphids (Myzus persicae)

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Molecular aspects of Potato Virus Y transmission by aphids (Myzus persicae)

Saman Bahrami Kamangar

A dissertation submitted in partial fulfillment of the requirements for the PhD degree in Bioscience Engineering

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Promoters:

Prof. dr. ir. Guy Smagghe, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University

Dr. ir. Kris De Jonghe, - Plant Sciences Unit, Flanders Research institute for Agriculture, Fisheries and Food (ILVO)

Dr. ir. Nji Tizi Clauvis Taning, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University

Dutch translation of the title:

Moleculaire aspecten van aardappel virus Y transmissie door bladluizen (Myzus persicae)

Please refer to this thesis as follows:

Bahrami Kamangar, S. (2021). Molecular aspects of Potato Virus Y transmission by aphids (Myzus persicae). PhD thesis. Ghent University, Belgium.

ISBN: 9789463574259

Ghent University:

Rector: Prof. dr. ir. Rik Van de Walle Faculty of Bioscience Engineering:

Dean: Prof. dr. ir. Marc Van Meirvenne

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Aknowledgment

During the preparation of this thesis, I received great support and assistance.

First, I would like to thank the Agricultural Research Education and Extention Organization (AREEO) in Iran for funding a part of my study.

I would like to extend my sincere thanks to my supervisors Prof. dr. ir. Guy Smagghe, Dr. ir. Kris De Jonghe and Dr. ir. Nji Tizi Clauvis Taning for their consistent encouragement, support and guidance over the running of this research.

I also wish to thank the Jury members Prof. Dr. Daisy Vanrompay, Dr. Olivier Christiaens, Dr. Jochem Bonte, and Dr. Stephan Steyer for reviewing and improving this thesis.

I am grateful to Steve Baeyen, Lab Manager at the Institute for Agricultural and Fisheries Research, for his technical support.

My wife Touba and son Siamand deserve special thanks for their patience, spiritual and emotional support. Without their understanding and encouragement in the past few years, it would have been impossible for me to complete my doctoral research.

I wish to thank my parents and sisters who supported and always gave me positive energy. I owe a great debt of gratitude to my brother Dr. Barzan Bahrami Kamangar for his encouragement and assistance when I was working on my PhD.

I gratefully acknowledge the help of my friends Dr. Khosro Mehdi Khanlou, Dr. Asad Maroufi, Serkewt Safaei, Dr. Amir Sadeghi, Hemen Piri and Dr. Hossein Hosseini Moghaddam.

Saman Bahrami Kamangar

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List of abbreviations

+ssRNA Positive-sense single-stranded RNA AAP Acquisition Access Period

AFP Acquisition Feeding Period ANOVA Analysis of variance

BCMV Bean common mosaic virus CaMV Cauliflower mosaic virus

CD Common duct

cDNA Complimentary DNA

CLSM Confocal laser scanning microscopy CMV Cucumber mosaic virus

CP Coat (capsid) protein

CPNP Circulative, persistent, non-propagative CPP Circulative, persistence, propagative CPR Cuticular protein family

CPR1 Cuticular protein 1 CuP Cuticular Proteins CYVV Clover yellow vein virus

DAS-ELISA Double Antibody Sandwich- Enzyme-Linked Immunosorbent Assay DNA Deoxyribonucleic acid

dsRNA Double-stranded RNA EPG Electric penetration graph

FC Food canal

GFP Green fluorescent protein

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HC Helper component

HC-Pro Helper component proteinase HIV Human immunodeficiency virus HR Hypersensitive response

IAP Inoculation access period

ICTV International Committee on Taxonomy of Viruses IgG Immunoglobulin G

JKI Julius Kühn Institute

IPM Integrated Pest Management

KITC (1 letter of Amino Acid codes) Lys-Ile-Thr-Cys KLSC (1 letter of Amino Acid codes) Lys-Luc-Ser- Cys KLTC (1 letter of Amino Acid codes) Lys- Leu-Thr- Cys KVSC (1 letter of Amino Acid codes) Lys-Val- Ser- Cys Mpcp Myzus persicae Cuticular Proteins

NCNP Non-circulative, non-persistent NCSP Non-circulative, semi-persistent NGS Next generation sequencing NP Nucleoproteins

ORF Open reading frame

P2 CaMV transmission protein

pC3 Nucleocapsid protein 3 RNA-binding viral protein of Rice stripe tenuivirus

PepMoV Pepper mottle virus

PepYMV Pepper severe mosaic virus PepYMV Pepper yellow mosaic virus

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PLRV Potato leaf roll virus PMV Peanut mottle virus PSV Peanut stripe virus

PTK (1 letter of Amino Acid codes) Pro-Thr-Lys PTNRD Potato tuber necrotic ringspot diseases PTV Peru tomato virus

PVA Potato virus A PVV Potato virus V PVX Potato virus X PVY Potato virus Y

PYBV Potato yellow blotch virus

QITC (1 letter abbreviation of Amino Acid) Gln -Ile-Thr- Cys RDP4 Recombination detection program (version 4)

RH Relative humidity

RITC (1 letter abbreviation of Amino Acid) Arg-Ile-Thr- Cys RJ Recombinant junctions (breakpoints)

RNA Ribonucleic acid RPS2 Ribosomal protein S2 RSV Rice stripe tenuivirus

RTTC (1 letter abbreviation of Amino Acid) Arg- Thr- Thr- Cys SBMV Soybean mosaic virus

SPFMV Sweet potato feathery mottle virus SOC Super Optimal Broth medium TA Transmission activation TEV Tobacco etch virus

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UPGMA Unweighted pair group method with arithmetic mean UV Ultra violet

VPg Viral protein genome-linked WPMV Wild potato mosaic virus Y2H Yeast-2-hybrid

YMV Yam mosaic virus

ZYMV Zucchini yellow mosaic virus

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Doctoral project context and research questions

A majority of plant viruses are dependent on vectors for their transmission and survival. Vectors that transmit plant viruses include mites, protists, fungi, insects and nematodes. Among these vectors, insects are the most common, with aphids accounting for the transmission of about 50% of insect-vectored viruses. Although vector-virus interaction is known to play a key role in the spread and epidemiology of plant viruses, several knowledge gaps still exist about the detailed mechanisms involved in the vector-virus transmission relationship. Potato virus Y (PVY) is an RNA virus and 5^th most damaging plant virus and causative agent of potato damage worldwide that infects a wide range of hosts but potato is the most important host (Scholthof et al., 2011). PVY is transmited in a non-circulative non-persistent (NCNP) manner by aphids. NCNP transmission is one of the simplest (still specific) transmission types and at the same time it has complexities and unknowns.

Transmission and strain variability are important components of PVY epidemiology with some unknowns and obscurities that still need to be understood in details. The questions about these obscurities inspired us to take a step towards better understanding PVY transmission in the following 3 topics that could improve knowledge of PVY epidemiology and management:

 Chapter 2 Identification of PVY strains in Belgium.

 Chapter 3 Understanding the relationship between PVY quantity in the stylet of aphid, rearing plants and PVY transmission efficiency.

 Chapter 4 Identification of PVY receptors in the aphid stylet.

PVY as an RNA virus is always changing and adapting to new environments and cultivars. This genetic diversity and new recombinants provide capacity to overcome PVY resistance in potato cultivars, and this has increased significantly in recent years.

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PVY strains induce a variety of symptoms in potato cultivars and the resistance is a cultivar-strain interaction. Due to lack of new information on the prevalence of PVY strains in Belgium, which plays a key role in the selection of resistant cultivars, breeding programs and the integrated management of the disease, it was important to update and collect new information on the diversity, occurrence and significance of prevalent strains. Chapter 2 is providing a survey on the presence of PVY strains in Belgium that are the main material in followed chapters of this thesis.

NCNP transmission of PVY and the presence of different aphid species as vectors promote the transmission of PVY in the farm, but the transmission efficiency of these aphids varies depending on the conditions and aphid entities. Behavioral factors (including food preference and host plant interaction) or the quantity of virus particles in the stylet (as the essential organ in PVY transmission) may be the most significant factors influencing transmission efficiency. In addition, limited studies indicate the inhibitory effects of various substances (also plant materials) on the transmission of PVY, although the mechanism remains uncertain. The transmission efficiency of PVY aphids can be affected by plants materials, so inhibition of virus lodging in aphid stylet may be one of the reasons for this. Assuming that the substances in aphid host plants before the virus is acquired will affect the virus content of the stylet and reduce the transmission efficiency of the virus, the effect of the host plant on the transmission efficiency and the quantity of viruses in the stylet of vector and non-vector aphids was evaluated in another section of this dissertation. The impact of host plants for aphid rearing (prior to virus acquisition) on virus quantity and transmission efficiency were evaluated as a part of this dissertation that is discussed in chapter 3.

The sequence of PVY genes is well known and the role of encoded proteins by these genes in the plant and in virus transmission (HC and CP) are well known, however,

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the biochemical details of receptors and behavior of aphid vectors in virus transmission are less known. The chemical properties of PVY receptor/s in aphids were unknown until recently. Indirect evidence from viruses with similar transmission mechanisms (NCNP and NCSP), such as ZYMV in the Potyvirus genus and CuMV in the Caulimovirus genus, indicated that the cuticle proteins (CuPs) in the distal part of the aphid stylet may be PVY receptors. Accurate detection of these receptors can be useful in PVY transmission prevention and management approaches.

RNAi has been used as an effective tool with a bright future (in managing pests and researching the biochemical cycles of living organisms) to recognize receptors involved in the transmission of viruses by silencing their genes. However, the diversity of cuticle proteins, the sequence similarity and their expression as gene families can impair the efficacy of this method. Chapter 4 is about the efforts of CuP genes silencing of most efficient vector of PVY (Myzus persicae) by means of dsRNA.

In the last chapter, the results of these studies and related recent findings in other laboratories were discussed to explain what we have added and what should be added to the knowledge of PVY in Belgium and around the world.

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Chapter 1 General introduction

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Chapter 1 General introduction

1.1. The potato plant as staple food

About 7,000 years ago, the Andes habitants in South America started gathering and experiencing potato tubers as a food. While the plants produce inedible true fruits, the tuber is, and produces enough energy-rich nutrients. The tubers also acted as a vegetative ‘seeds’ and the early humans in Andes discovered how to propagate the crop. They started to transport and store the tubers for feeding of the society and they learned to plant and grow potato gradually. Today’s potato (Solanum tuberosum) has been selected from S. brevicaule populations from the Andean region and nowadays has become one of the most important staple foods in the world (Navarre and Pavek, 2014).

Figure 1.1. Total production, yield and area harvested of potato in Belgium (2000-2018). https://www.fao.org/faostat/en/#data

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Potato has been cropped on 65,000-98,000 ha (13-15% of total crop lands) in Belgium since 2000-2019. It is the second most produced commodity after the wheat, range from 3.4 to 4.4 million tons, which is about 0.7 to 0.9% of world production and put Belgium in 22^nd ranks in the world (Faostat, 2021). The potato crop has been affected by drought in rainfed systems, as was the case in Belgium in 2018, resulting in a 30%

loss of the crop (Sawyer et al., 2019). The high edible energy and dry matter of potato (per ha per day) (Fig. 1.1 and 1.2) makes it the biggest production value crop (US$/ha/day) compared to the other main staple food crops (wheat and rice) (Roots, tubers, plantains and bananas in human nutrition - Nutritive value, 2021).

1.2. Plant viruses

Viruses as assembled genetic materials (RNA or DNA) in coat protein subunits the nucleoproteins (NP) and sometimes enveloped in lipoprotein membranes. They are non-living obligate parasites that start replication only in suitable host cells and use own genes to exploit the host cells and profit from ribosome and other protein production systems and structural materials present in the host cell, for its replication

Figure 1.2. Comparison of harvested area and production of wheat and potato in Belgium (2018).

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and cell to cell movement (Hull, 2014). They have specialized and adapted to different types of host cells including plants. A wide diversity of plant viruses consisting of a variety of different shapes and sizes, as well as different types of genetic materials (Fig. 1.3), cause important diseases in many crops, and result in major economic losses all over the world (Agrios, 2005). The economic impact of plant viruses on crops is higher than what it seems to be, because the symptoms could be confused with nutrient deficiencies, abiotic stress, herbicide and hormone damage or its vector damage in plants. (Scholthof, 2011; Hull, 2014).

The plant viruses can't enter host tissues by themselves to multiply and propagate and must be carried and facilitated to enter living cells and introduce a new plant infection.

Unlike for animal viruses, virus movement in the plants is restricted to plasmodesmata.

They can’t enter or exit from membrane protected cells directly, since they are bound by a strong cell wall, composed by pectin and cellulose (Benitez-Alfonso et al., 2010).

They rely on a third party to spread between same or to next generations of host plants by means of mechanical wounds of contaminated instruments, or feeding and/or parasitizing arthropods, nematodes, parasitic plants and fungi-like vectors (Mukhopadhyay, 2011). Moreover, they infect plant progenies during sexual (true seeds and pollen) and vegetative reproduction, with the last pathway the most likely to transmit the viruses. A high rate of virus spread and transport over long distance by vegetative reproduction organs, can increase virus importance in the crops such as potato. A case study on potato viruses pointed out that infections with potato leaf roll virus (PLRV), annually cause about £30 - 50 million losses in UK alone (Hull, 2014).

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Viruses are classified by International Committee on Taxonomy of Viruses (ICTV) and Figure 1.3. Diversity in genetic material and morphology of plant virus.

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currently include 4 realms, 9 kingdoms, 16 phyla, 2 subphyla, 36 classes, 55 orders, 8 suborders, 168 families, 103 subfamilies, 1421 genera, 68 subgenera, 6590 species of which about 2, 3, 7, 12, 16, 34 (+6 unassigned), 127 (+45 unassigned) and 1624 are plant virus realms, kingdoms, phyla, classes, orders, families, genera, and species respectively. In addition, to date, 33 viroids and 143 satellite viruses that cause virus- like symptoms or modify virus symptoms are classified as virus-associated organisms (ICTV master species list 2019.v1, 2021). Recent studies based on high-throughput sequencing (HTS) technologies (next generation sequencing) are “discovering novel viruses” at an increased pace, because of the vast amount of data that are being generated in a short time frame, and because former studies mainly focused on eminent problems caused by symptomatic viruses resulting in latent or cryptic viruses being ignored (Massart et al., 2017; Adams et al., 2018; Maclot et al., 2020; Rubio et al., 2020). Some of these viruses in a co-evolution process together with the plant host have gained a stable condition as persistent cytoplasmic viruses. They do not transmit horizontally, do not move from cell to cell and only infect their hosts for many generations vertically. Some sequences of the genome of these viruses have integrated with genomes of the host plants and they could increase the plant abilities (Roossinck 2012b; Schoelz and Stewart 2018). The most diverse plant virus families are those of the begomoviruses (Geminiviridae) and potyviruses (Potyviridae) respectively (Genus: Begomovirus, 2021; Genus: Potyvirus, 2021). The nucleic acid properties (RNA or DNA, double or single stranded, the sense and segment of the genome), morphology and structure of the virion, genome sequence homology, biological and serological properties are the most important characteristics used to discriminate different levels of virus taxa (King et al., 2012) (Fig 1.4).

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Figure 1.4. Potyviridae phylogenetic tree. Pairwise unrooted neighbor-joining tree of complete polyprotein sequences of representative viruses within the family Potyviridae. The tree was produced in MEGA 7 Branches supported by

>70% of 100 bootstrap replicates are indicated. (Adapted from: Potyviridae, 2021)

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1.2.1. Plant virus transmission

The transmission of viruses takes place by sexual or vegetative propagation, mechanically and/or through vectors. Knowledge on the transmission modes are essential to grasp virus diversity and evolution, as well as a critical step in surveillance (da Silva et al., 2020). Mechanical transmission takes place in different ways. Plant viruses move from infected plants to wounded healthy plants in a same generation and/or the same growing season (horizontal transmission), and this through direct contact with contaminated soil, water, tools and/or plant tissues (roots and foliage) (Fageria et al., 2015). Survival and transmission of viruses in at least 7 genera have been detected in water of canals, lakes and even oceans and in soils including for carmoviruses, cucumoviruses, diathoviruses, tobamoviruses, necroviruses, potexviruses, tombusviruses and sobemoviruses, all among the most stable viruses to survive outside a host plant (Mehle and Ravnikar, 2012; Hull 2014; Mehle et al., 2014). In addition, some of these plant viruses were tracked in processed food (e.g.

pigmented sauces), humans and wild animal guts and feces, (Zhang et al., 2005;

Rosario et al., 2009; Li et al., 2010; Phan et al., 2011; Scheets et al., 2011; Roossinck, 2012a and b). On the other hand, some viruses are difficult, or even completely fail to be transmitted mechanically, especially those that are restricted to trachea (xylem or phloem), e.g. members of the Closteroviridae (Walkey, 1991).

Transmission to the next generation (vertical transmission) is possible by infected vegetative propagules (bulb, tuber, scion, grafts, rootstocks) and /or sexual (pollen and seed) propagation (Walkey, 1991). About one-seventh of all plant viruses are known to be transmissible through infected seeds, the basic input for most cultivated crops in agriculture, and are responsible for virus transmission over longer distances and time periods. In addition, they not only reduce seed germination, but also plant

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vigor. Infected seed coats (e.g. for tobamoviruses) and/or embryo (e.g. potyviruses) induce plantlet infection mechanically or systemically (Hamelin et al., 2017). More than 231 virus species are transmitted by seeds, mainly in Potyvirus, Nepovirus, Cryptovirus, Ilarvirus, and Tobamovirus genera (Sastry 2013; Hull 2014). In addition to seeds, plant pollen has been confirmed as a source of transmission for several virus genera, including members of the genera Alphacryptovirus, Alfamovirus, Anulavirus, Badnavirus, Cheravirus, Comovirus, Cucumovirus, Hordeivirus, Idaeovirus, Ilarvirus, Nepovirus, Nucleorhabdovirus, Potyvirus, Sobemovirus, Tepovirus, Tobravirus, Tymovirus, as well as viroids belonging to the genus of the Avsunviroid, Hostuviroid and even Pospiviroid (Das et al.,1961; George and Davidson, 1963; Gilmer and Way, 1963; Wang et al.,1993; Liu et al., 2014). Pollen is easily dispersed over a long distance by wind, honey bees and other pollen carriers like bumble bees,hoverflies, nectar scarabs and even thrips and are able to transmit some viruses to seeds and mother plants as well (Hull, 2014; Levitzky et al., 2019). Furthermore, dodder species (Cuscuta spp.) parasitize many plants genera and are capable of transmitting plant viruses between adjacent plants as a bridge. Dodders are used as an experimental tool to transmit the viruses when they fail to be transmitted by other methods (largely mechanical) in the lab (Walkey, 1991). Some viruses may infect dodder cells and a low percent of seeds (Mikona and Jelkmann, 2010; Hull 2014).

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Based on the virus characteristics, being non-living obligate parasites, they often need to be acquired, transmitted and re-entered from infected plants to a living cell of new plants during an active process through vectoring by a diverse group of living organisms. Some species in arthropods (insects and mites), nematodes, fungi, and fungi-like organisms (protists zoosporic endoparasites) are among important so-called plant virus vectors. Mites, and mainly insects (aphids, thrips, whiteflies, leafhoppers, planthoppers, treehoppers, mealybugs and mirids) (Fig. 1.5) are the most common plant virus vectors. Nearly 450 aphid species that have a complex life cycle feed on sap of a diverse group of plants (about 5000 plant species), among them crop plants.

They are considered as crop pests to be the most important plant virus vectors as around 190 aphid species transmit over 300 virus species (of which 100 economically important ones) in different modes (persistent, semi-persistent and non-persistent) (Emden and Harrington, 2017; Lacomme et al., 2017).

Figure 1.5. The percentage of viruses that can be transmitted by different vectors (Syller 2014)

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The complex structure of aphid mouth parts are specialized for sucking of plant saps (Fig. 1.6). The two mandibles combine and form an outer stylet and maxillae join and piece to make inner stylet with canals including food and saliva ducts. These two canals join together and form common duct in the tip of the inner stylet that include a dense cuticular structure named acrostylet. This complex is wrapped in the labium at rest and when the aphid start feeding the sheath draw back and the stylet structure pierce the plant tissue as a needle (Harris and Maramorosch 1977). The saliva is injected from the saliva canal and plant sap is sucked up through the food canal.

Aphids inject two types of saliva, gel and watery, during plant sap sucking (Harmel et al., 2008). These two types of saliva involve in the different modes of virus transmission, as reviewed by Fereres (2007).

Aphids produce different morphological types during their life cycle (Moran, 1992;

Blackman and Eastop, 2000; Williams and Dixon, 2007). Most aphids may reproduce Figure 1.6. Stylet structure of aphids, Colored in yellow are maxillae, red are mandibels

and green is labium. Adapted from (Taylor and Robertson, 1974; Uzest et al., 2010)

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both sexually and by parthenogenesis during their life cycle, which is called holocyclic, whereas some aphids are by parthenogenesis only. The aphids may produce various morphs throughout their life cycles including egg, nymphs, alate (winged or dispersing), apterous (wingless or non-dispersing) and brachypterous (having very short or incompletely-developed wings). Different environmental conditions trigger to change wingless to winged generation and vice versa. Among these triggers are aphid density, host plant quality (at least in some species), interspecific interactions, and environmental conditions (such as temperature, light and photoperiod) (cited in Braendle et al., 2006). Some aphids (not all) produce winged forms (male and female) to move to new plants in case of crowding, nutritional and/or environmental pressures (temperature, precipitation and light intensity) (Giordanengo et al., 2013).

Virus transmission by vectors as a specific molecular interaction show a range of species specificity. Some viruses can be transmitted by many vector species while some are only transmitted by a single vector species (Ng and Perry, 2004; Hogenhout et al., 2008; Bragard et al., 2013; Hull 2014; Syller, 2014).

Plant virus transmissions by insect vectors take place in four steps, including acquisition, latent period, retention, and inoculation. Specific variability in virus vector interaction result in a different transmission mode (Table 1.1). One of the important characteristics to categorize the mode of transmission is the virus retention site (stylet, foregut, gut and hindgut) and the route of virus circulation in the vector body (Watson and Robert 1939; Kennedy et al., 1962; Nault and Ammar 1989; Katis et al., 2007).

The most widely accepted criteria for classifying and categorizing virus transmission modes are based on the following factors:

 The Acquisition Access Period (AAP) or Acquisition Feeding Period (AFP) is the time required between virus acquisition (by accessing or starting to feed)

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and the ability of the virus transmission to new plants by vectors.The time required between the access of the virulifer vector to plants and the inoculation of the virus to plants is referred to as the Inoculation Access Period (IAP).

 The longevity of the retention of the virus (being a vector virulifer) ranges from minutes to a lifetime, and can even include inheritance by the offspring.

 The location of retention and routing of the virus in the vector may be external (surface cuticle) or internal (hemolymph and salivary gland) interactions.

 The molecular component of virus retention and replication in the body of vectors.

 The latent phase of vectors is the interval between the acquisition of the virus by vector from the infected plant and the ability to transmit the virus.

On the basis of the aforementioned parameters, the transmission mode of the virus is categorized by Hull (2014) as below:

 Non-circulative, non-persistent (NCNP)

 Non-circulative, semi-persistent (NCSP)

 Circulative, persistent; non-propagative (CNP)

 Circulative, propagative (CPP).

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Table 1.1. Plant virus vectors and types of transmission.

Vector Transmitted virus

Family: Genera

Mode of

transmission References

Protists

Plasmodiophoral es:

Spongospora, Polymyxa

Virgaviridae: (Pomovirus, Furovirus (rod-shaped), Pecluvirus)

Benyviridae: Benyvirus zoospores internally

Campbell 1996;

Rochon et al., 2004; Bragard et

al., 2013 Potyviridae: Bymovirus (filamentous)

Fungi

Olpidiaceae:

Olpidium

Varicosavirus (non-enveloped rod

shape) zoospores Campbell 1996;

Rochon et al., 2004; Alfaro- Fernandez et al., 2010; Bragard et al., 2013; Hull

2014 Aspiviridae: Ophiovirus

zoospores Tombusviridae: Carmovirus

Alphaflexiviridae: Potexvirus

(Filamentous) few species zoospores Rhizoctonia

solani

Bromoviridae: Cucumber mosaic

virus Mycelium Andika et al.,

2017

Nematodes

Longidoridae:

Longidorus, Paralongidorus

Xiphinema

Secoviridae: Nepovirus, Cheravirus

persistent

van Hoof 1970, Karanastasi et al.,

2000; Vellios et al., 2002;

MacFarlane, 2003; Andret-Link

et al., 2004;

Holeva and MacFarlane, 2006 Trichodoridae:

Trichodorus, Paratrichodorus

Virgaviridae: Tobravirus

Mites Eryophidae

Potyviridae: Tritimovirus, Rymovirus, Poacevirus

semi- persistent

Oldfield 1970;

Kitajima et al., 2010, 2014;

Bragard et al., 2013;Solo et al.,

2020;

Betaflexivirida: Trichovirus Alphaflexiviridae: Allexivirus Secoviridae: Nepovirus (subgroup C)

Teneopalpidae Rhabdoviridae: Dichorhavirus persistent- propagative Fimoviridae: Emaravirus

Chewinginsect: (Beetles)

Beetles:

Chrysomellidae, Coccinellidae, Curculionidae and Meloidae

Secoviridae: Comovirus,

non- circulative, foregut-borne

(semi- persistent)

Gergerich, 2001;

Raccah and Fereres, 2009;

Mukhopadhyay, 2011; Tolin et al.,

2016;

Solemoviridae: Sobemovirus, Tymoviridae: Tymovirus, Tombusviridae: Carmovirus

Bromoviridae: Bromovirus

Sucking insect

Pseudococcidae (Mealybugs) and Coccidaev (Soft

scales)

Closteroviridae: Ampelovirus

semi-

persistent Hull, 2014 Caulimoviridae: Badnavirus

Leafhopper (Cicadelidae)

Caulimoviridae: waikaviruses and badnaviruses

semi- persistent

Ammar and Nault 2002; Hull 2014;

Whitfield et al., 2015, 2018 Geminiviridae: mastreviruses, and

curtoviruses

persistent circulative Rhabdoviridae: Marafiviruses,

Nucleorhabdovirus, Cytorhabdovirus, Phytoreovirus

persistent- propagative Phenuiviridae: Tenuivirus

planthopper (Delphacidae)

Tymoviridae: Marafivirus

persistent- propagative Rhabdoviridae: Nucleorhabdovirus,

Reoviridae: Fijivirus Phenuiviridae: Tenuivirus planthopper

(Cixiidae) Nanoviridae: Nanovirus persistent circulative

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Treehopper (Membracidae)

Gemeniviridae:Topocuvirus, Curtovirus,

persistent circulative

Ammar and Nault 2002; Hull 2014;

Whitfield et al., 2018

Whitefly (Aleyrodoidea)

Secoviridae:Torradovirus, semi-

persistent Jones 2005;

Czosnek and Ghanim 2012 Gemeniviridae: Begomovirus, persistent-

circulative Betaflexiviridae: Carlavirus, semi-

persistent

Jeyanandarajah and Brunt 1993;

Mansour and Almusa 1993;

Webb et al., 2012 Closteroviridae: Crinivirus

Potyviridae: Ipomovirus non-persistent

Bugs:

Piesmatidae, Miridae, Orsillidae (Lyga eidae: Orsillinae

) and Pentatomidae

Rhabdoviridae: Nucleorhabdovirus propagative

persistently Proeseler 1980 Potyviridae: potyvirus non-persistent Odedara et al.,

2007 Solemoviridae: Sobemovirus

( velvet tobacco mottle virus)

persistent- circulative

Gibb and Randles 1988; Gibb and

Randles 1991 Potyviridae: Longan witches broom-

associated virus Un-assigned species

circulative mode in salivary glands

Chen et al., 2001;

Seo et al., 2017

Thrips (Thysanoptera)

Thripidae

Bunyaviridae:Tospovirus

persistent- propagative,

transovarial transmitted

Jones, 2005 Tombusviridae: Machlomovirus semi-

persistent Solemoviridae: Sobemovirus pollen-carried

by thrips Ilarviruses: Ilarvirus

Aphids (Aphididae)

Betaflexiviridae: Carlavirus non-persistent

Ng and Perry 2004; Sanfacon et al., 2012; Bragard et al., 2013; Valli

et al., 2017 Bromoviridae: Alfamovirus,

Cucumovirus

non-circulative capsid strategy Caulimoviridae: Caulimovirus

semi- persistent helper strategy Closteroviridae: Closterovirus semi-

persistent Comoviridae: Fabavirus non-persistent Luteoviridae: Enamovirus,

Luteovirus, Polerovirus

circulative non propagative Nanoviridae: Nanovirus, Babuvirus

circulative non- propagative Potyviridae: Macluravirus, Potyvirus non-circulative

helper strategy Rhabdoviridae: Cytorhabdovirus,

Nucleorhabdovirus

circulative propagative Secoviridae: Waikavirus, Sequivirus

non-circulative semi- persistent

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Non-circulative non-persistent transmission (NCNP)

NCNP viruses tend to infect all plant cell types during feeding and can be acquired from the infected plant and transferred to the recipient plant after AAP and IAP, respectively, within seconds to minutes by their vectors. These viruses are transmitted by the vector stylet when piercing the epidermal cells in order to find the desired plants and the vectors remain viruliferous for minutes to hours, depending on temperature and further feeding (Pirone, 1977; Roossinck, 2010). They lose their transmissibility as the vector molts or feeds on healthy plants for a few times (Nault and Styer, 1972, Powell and Hardie, 2000). During the virus transmission the virus particles don’t circulate (transit) across the vector body and the involved viral particles in the transmission are only retained in the tip of the insect stylet, and in the common duct (mainly aphid vectors). This may be mediated by interaction of the coat protein and vector receptor (Capsid-dependent) or by complex interactions, including coat protein, helper protein/s and vector receptor (Helper component mediated). Studies based on electrical penetration graph (EPG) and potential drop (pd) waveform revealed that NCNP potyviruses are inoculated by aphid vectors during superficial brief intracellular punctures in the early host plant evaluation.

NCNP viruses acquire during sub-phases II-3 (third intracellular activity) and inoculate efficiently in sub-phases II-1 (first intracellular activity) during active saliva injection into the plant cells by aphids vectors (Martin et al., 1997; Powell, 2005;

Moreno et al., 2012). Alfamovirus, Bromovirus, Carlavirus, Cucumovirus, Fabavirus, Macluravirus, Potexvirus, and Potyvirus are the most important NP viruses (Pirone and Perry, 2002; Bragard et al., 2013).

Persistent circulative, non-propagative transmission (CNP)

The persistently transmitted viruses, including Luteoviridae, Geminiviridae,

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Nanoviridae, and Reoviridae, are transmitted by aphids, leaf- and treehoppers, and whiteflies. This type of transmission is more specific compared to non-persistently transmitted viruses. They are acquired and inoculated from and to the plant phloem within hours to days. Acquisition period can be roughly 5 min to hours, but at least a 12 h latency period is required from acquisition to inoculation, after which they can be inoculated in a timeframe of about 10-30 min, e.g. for aphid vectors transmitting luteoviruses (Hull, 2014). The retention time may last from a few days to the whole life span of the vectors, and may be retained even after molting. Virus particles must circulate and pass from the gut lining to the hemolymph and neighboring organs, and then to the accessory salivary glands of the vectors, after which the virus can be inoculated to the new plant host (Zhou, 2018). More than for the interactions between viruses themselves, plant and vector proteins, and sometimes extra proteins from other viruses (helper viruses) or even bacteria (Buchnera spp.) are needed to facilitate the transmission of these viruses (Gonçalves et al., 2005; Hull, 2014; Cilia et al., 2011;

2014), although the results of some studies raise doubts about the involvement of Buchnera proteins in the transmission of Luteovirus (Bouvaine et al., 2011).

Non-circulative semi-persistent transmission (NCSP)

NCSP viruses possess features of the NCNP and CPNP viruses, and the virus particles circulating in the vector body and/or retained on the surface of the chitin lining at the tips of the stylet (common duct) or in the foregut of the insect vectors, are transmitted. The vectors do not transmit the virus after molting, and circulation of the virus through the body of the vector is not a requirement for transmission (Zhou, 2018).

They are often present in phloem, and AAPs, IAPs and retention periods (h to days) are typically longer than those of NP viruses. Details of this virus transmission mode are not well understood and there are still some obscurities (Childress et al., 1989;

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Uzest et al., 2010; Chen et al., 2011; Ng, 2013; Li et al., 2016; Zhou et al., 2018).

Although some species of the genera Closterovirus, Crinivirus and Caulimovirus are SP-type transmitted viruses, they use different sets of proteins and/or binding sites for transmission. Inoculation of NCSP viruses takes place during sub-phase II-2 in aphids, but they may also be transmitted by different vectors such as leafhoppers, aphids and whiteflies (Uzest et al., 2010; Moreno et al., 2012; Hull, 2014).

Persistent circulative, propagative transmission (CPP)

Propagative transmissible plant viruses enter and replicate in the insect vectors, and so, in this case, both plants and vectors may be considered to be hosts of the virus.

They are retained for days to a lifetime (even after molting vectors) and, depending on the virus, they infect various vector organs and even transmit transovarially to the offspring. This mode of transmission is extremely specialized and viruses are transmitted by a single species of insect vector. The propagative transmissible plant viruses are listed below. Marafivirus, Nucleorhabdovirus, Cytorhabdovirus, Tenuivirus, Phytoreovirus, Fijivirus, and Oryzavirus are transmited by vectors belonging to the Cicadellidae, Delphacidae, and Membracidae families, namely plant-, leaf- and treehoppers (Hohn 2007; Blanc et al., 2014; Hull ,2014; Whitfield et al., 2015; Dader et al., 2017).

1.2.2. Plant virus symptoms

Several hundreds of plant viruses on a vast number of plants with visible symptoms or invisible signs have been reported. Reports on virus presence without producing symptoms, so-called latent viruses, have been increasing since new techniques such as HTS became more commonly available in plant virus diagnostics (Adams et al., 2018). The type and severity of symptoms are determined by type of virus (species and strains) and mainly the host plant (species, variety, resistance to the virus, virus

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infection and plant age) (Kaplan and Meier, 1958; Funke et al., 2017; Ali and Abbo, 2019; Dupuis et al., 2019). Moreover, environmental conditions (Roossinck, 2015) and virus co-infection with other viruses or plant pathogens (Syller, 2012) affect the plant symptoms induction. Plant symptoms induced by viruses are yellowing and reddening, mosaic, stunting and dwarfing, distortion, crinkle, flower color breaking, local lesions and ring spots, vein clearing and necrosis, vein banding, hypertrophy and hypotrophy, leafroll and leaf curl, epinasty and big-vein (Agrios, 2005; Hull, 2014).

1.2.3. Important potato viruses

Vegetative propagation of potato and accumulation of different viruses in tubers degenerate seed tubers and impose high costs to virus elimination by means of some methods like tissue culture (Thomas-Sharma et al., 2015). About 50 virus species infect potato and cause an important crop losses, however, they rarely kill the potato plants (Wale et al., 2008). The reported naturally occurring plant viruses (and viroids) in potato worldwide are listed in Table 1.2.

Table 1.2. The viruses infecting potato (S. tuberosum)

No.

Name (Abbreviation)

Taxonomy (Order, Family, Genus)

Distribution

Losses significance

Vector References

1

Alfalfa mosaic virus (AMV)

Unassigned, Bromoviridae,

Alfamovirus

Worldwide

Little economic importance

Aphid

Stevenson et al., 2009

2

Andean potato latent virus

(APLV)

Tymovirales, Tymoviridae, Tymovirus

S America Little damage Beetles

Koenig et al.,1979

3

Andean potato mottle virus

(APMoV)

Picornavirales, Secoviridae,

Comovirus

S America

may be significant

Contact

Dusi and Avila, 1988

4

Arracacha virus B-oca strain

Cheravirus, (tentative), Sequiviridae

Peru, Bolivia Unknown Unknown

Jones, 1981

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(AVB-O)

5

Beet curly top (BCTV)

Unassigned, Geminiviridae,

Curtovirus

Arid areas Worldwide

Leafhoppers King et al., 2012

6

Cucumber mosaic virus

(CMV)

Cucumovirus

Worldwide

Aphid

Chrzanowska et al., 2003

7

Eggplant mottled dwarf virus

(EMDV)

Mononegavirales, Rhabdoviridae, Nucleorhabdovirus

Iran

Rare in potatoes

Aphid Danesh, 1989

8

Groundnut bud necrosis virus

(GBNV)

Unassigned, Bunyaviridae,

Tospovirus

India Unknown Thrips Jain ey al., 2004

9

Groundnut ringspot virus

(GRSV)

Tospovirus

Argentina Unknown Thrips

Bragard et al., 2020

10

Impatiens necrotic spot

virus (INSV)

Tospovirus

USA Unknown Thrips

Crosslin and Hamlin, 2010

11

Potato aucuba mosaic virus

(PAMV)

Tymovirales, Alphaflexiviridae,

Potexvirus

Worldwide Unknown Contact, aphids

Susaimuthu et al., 2007

12 Potato black ringspot virus

Nepovirus

S America Unknown Unknown Richards et al., 2014

13

Potato black ringspot virus

(PBRSV)

Nepovirus

Peru

Low importance in

potato

Nematodes Salazar and Harrison 1978

14

Potato deforming

mosaic (Argentina)

(PDMV)

Geminivirus,

Begomovirus, tentative, Brasil Up to 35 % Whitefly Bragard et al., 2020

15 Potato latent virus (PotLV)

Tymovirales,Betaflexiviridae,

Carlavirus N.America Unknown Aphid Nie, 2009

16 Potato leaf rollvirus (PLRV)

Unassigned,

Luteoviridae, Polerovirus Worldwide up to 90% Aphid De Boer et al.,1996

17 Potato mop top virus (PMTV)

Unassigned, Virgaviridae, Pomovirus

N and C Europe Peru

Affect tuber

quality Fungi Stevenson et al., 2009

18

Potato rough dwarf virus

(PRDV)

Tentative, Carlavirus Argentina Uruguay

Little

importance Aphid Massa et al., 2008

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19

Potato spindle tuber viroid

(PSTVd)

Unassigned, Pospiviroidae,

Pospiviroid

Europe

64 % (Pfannenstiel,

1980)

Contact and aphid when Coinfected with PLRV

Pfannenstiel, 1980

20 Potato virus A (PVA)

Unassigned, Potyviridae, Potyvirus

Worldwide Can be up to

40 % Aphid De Boer et

al.,1996

21 Potato virus M (PVM)

Tymovirales, Betaflexiviridae,

Carlavirus

Worldwide at worst 15 -45% Aphid De Boer et al.,1996

22 Potato virus P (PVP)

Carlavirus

Brasil

20 - 80 % importance

local

Aphid Bragard et al., 2020

23 Potato virus S (PVS)

Carlavirus

Worldwide At worst 10 -

20 % Aphid De Boer et

al.,1996

24 Potato virus T (PVT)

Unassigned

S America

(Peru) Unknown Contact Bragard et al., 2020

25 Potato virus U (PVU)

Nepovirus

Peru Unknown Nematodes Bragard et al., 2020

26 Potato virus V (PVV)

N.America S.America

Damage

severe Aphids Oruetxebarria et at. 2000

27 Potato virus X (PVX)

Tymovirales, Alphaflexiviridae,

Potexvirus

Worldwide Usually

15 -20% Contact De Boer et al.,1996

28 Potato virus Y (PVY)

Worldwide Losses reach 10-80 %

Aphid Bragard et al., 2020

29

Potato yellow dwarf virus

(PYDV)

Mononegavirales, Rhabdoviridae, Alphanucleorhabdovirus

N.America No economic

importance Leaf hopper Anderson et al., 2018

30

Potato yellow mosaic virus

(PYMV)

Unassigned, Geminiviridae,

Begomovirus

Carribean

region Unknown Whitefly Morales et al., 2001

31

Potato yellow vein virus

(PYVV)

Unassigned, Closteroviridae,

Crinivirus

S America (Columbia Venuzuela Peru and

More than 50 % Whitefly Salazar et al., 2005

32 Potato yellowing

virus (PYV) Tentative, Alfamovirus S America Unknown Aphid Silvestre et al., 2011

33

Potato yellow blotch virus”

(PYBV)

UK Unknown Aphid

Bragard et al., 2020; Nisbet et

al., 2018;

Kreuze et al., 2020 34 Solanum apical

leaf curling virus Tentative, Geminivirus Peru Significance in

localized Aphid Hooker and Salazar 1983

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(SALCV) areas

35 Sowbane mosaic virus (SoMV)

Sobelivirales, Unassigned, Sobemovirus

Worldwide Rare in

potatoes Unknown

Bragard et al., 2020; Kreuze et

al., 2020

36

Tobacco chlorotic spot

virus (TCSV)

Tospovirus

Argentina

Brazil Unknown Unknown

Bragard et al., 2020; Kreuze et

al., 2020

37 Tobacco mosaic virus (TMV)

Unassigned, Virgaviridae, Tobamovirus

Worldwide Not problem in

potatoes Contact Jung et al., 2002

38

Tobacco necrosis virus

(TNV)

Unassigned, Tombusviridae,

Necrovirus

Europe, N.America,

Tunisia

Not significance in

potatoes

Olpidium brassicae

Beuch et al., 2013

39 Tobacco rattle virus (TRV)

Unassigned, Virgaviridae, Tobravirus

Worldwide May be

appreciable loss Nematodes David et al., 2010

40 Tobacco streak virus (TSV)

Ilarvirus

S America

Little significance in

potatoes

thrips Salazar et al.,1982

41 Tomato black ring virus (TBRV)

Nepovirus

Europe Little

significance Nematodes Kaiser, 1980

42

Tomato leaf curl New Delhi virus

(ToLCNDV)

Unassigned, Geminiviridae,

Begomovirus

India Unknown whitefly Usharani et al., 2004

43 Tomato mosaic virus (ToMV)

Unassigned, Virgaviridae, Tobamovirus

Hungary Not problem in

potatoes Contact

Yazdani- Khameneh et

al., 2013

44

Tomato mottle Taino virus

(ToMoTV)

Begomovirus

Cuba Unknown Whitefly Cordero et al., 2003

45 Tomato spotted wilt virus (TSWV)

Tospovirus

Worldwideh ot climates

Importance in

Localized areas Thrips Abad et al., 2005

46

Tomato yellow fruit ring virus

(TYFRV)

Bunyaviridae,

Tospovirus Iran Unknown Thrips Golnaraghi et

al., 2008

47 Tomato yellow ring virus (TYRV)

Bunyaviridae,

Tospovirus Poland Unknown Thrips Birithia et al.,

2012

48

Tomato yellow vein streak virus(ToYVSV)

Begomovirus

Brazil Unknown Whitefly

Ribeiro et al., 2006

49

Wild potato mosaic virus

(WPMV)

Unassigned, Potyviridae,

Potyvirus - No problem in

potatoes Aphids Fribourg et al., 2019;

50

Pepino mosaic virus (PepMV)

Tymovirales, Alphaflexiviridae,

Potexvirus

- Not infected

potato naturally Contact Bragard et al., 2020

Molecular aspects of potato virus Y transmission by aphids (Myzus persicae)