Christophe Lacomme - Academia.edu (original) (raw)

Papers by Christophe Lacomme

Achieving sustainable cultivation of potatoes Volume 2, 2018

The aim of the VirusCollect II project was to establish and extend an international network of co... more The aim of the VirusCollect II project was to establish and extend an international network of collections of plant viruses and viroids thereby making virus isolates available for reference at diagnostic and research laboratories in Plant Health. At present access to isolates of regulated viruses is limited and only the plant virus collection at DSMZ is officially accredited as reference producer. Strengthening the infrastructure of plant virus collections is required because diagnostic tests on regulated organisms have to be accredited under the new Plant Health rules of the European Union that apply from December 14^th 2019. The ability of laboratories of National Plant Protection Organizations (NPPOs) to fulfil this requirement will depend on public access to well-characterised virus isolates. The collaboration between partners of the Euphresco projects NGS-detect and VirusCollect II and especially their joint meetings offered a fruitful platform for exchang...

The worldwide prevalence of Potato virus Y (PVY) poses a continuous challenge to efficient potato... more The worldwide prevalence of Potato virus Y (PVY) poses a continuous challenge to efficient potato production. The accurate diagnosis of viruses such as PVY is inherently challenging due to the broad biological and genetic diversity of PVY strains that elicit a range of symptoms and diseases in various potato cultivars and related solanaceous species. A wide range of techniques have been developed over a period of 50 years for the detection of PVY. Serological methods such as ELISA, using polyclonal and especially monoclonal antibodies, have been widely used by most diagnostic laboratories, due to their cost effectiveness and capacity to implement for a large number of samples. Over the last decade, PCR-based assays have been routinely used in diagnostic laboratories because of their sensitivity, specificity and their capacity to be automated for high-throughput testing. The objective of this chapter is to provide a brief historical overview of the main diagnostic methods used to det...

Diseases caused by plant viruses can have significant and devastating impacts on many cultivated ... more Diseases caused by plant viruses can have significant and devastating impacts on many cultivated crops worldwide. The impact of disease caused by a virus depends on the virus species, strains, type of inoculum, host plant characteristics, vector pressure, climatic conditions, trade, changes in agricultural landscape and intensive production practices. Viruses affect plants by causing a large variety of symptoms such as alteration of shape, pigmentation, necrosis on different parts of the plant, thus affecting plant development. In most of the cases, these lead to a decrease in crop yield and quality. There are numerous viruses that affect potato; among them, Potato virus Y is considered to be one of the ten most important plant viruses of crops, because of its worldwide distribution and economic impact. Some PVY isolates are able to cause potato ringspot necrotic disease in infected tubers rendering them unmarketable. Understanding the genetic diversity and molecular biology of PVY ...

RSC Chemical Biology, 2020

A novel DNA sensing method based on LD spectroscopy and using bionanoparticle scaffolds is descri... more A novel DNA sensing method based on LD spectroscopy and using bionanoparticle scaffolds is described, as demonstrated by the rapid detection of DNA strands associated with bacterial and viral pathogens.

Methods in Molecular Biology, 2015

EFSA Journal, 2020

Following a request from the EU Commission, the Panel on Plant Health has addressed the pest cate... more Following a request from the EU Commission, the Panel on Plant Health has addressed the pest categorisation of non-EU isolates of potato virus X (PVX). The information currently available on geographical distribution, biology, epidemiology, potential entry pathways, potential additional impact and availability of control measures of non-EU isolates of PVX has been evaluated with regard to the criteria to qualify as a potential Union quarantine pest. Because non-EU isolates of PVX are absent from the EU, they do not meet one of the requirements to be regulated as a regulated non-quarantine pest (RNQP) (presence in the EU); as a consequence, the Panel decided not to evaluate the other RNQP criteria for these isolates. On the basis of their ability to overcome potato resistance genes, PVX isolates can be divided into several pathotypes. PVX isolates that are not able to overcome resistance genes and PVX isolates that are able to overcome the Nb and/or Nx resistance genes are already present in the EU. Isolates able to overcome the Rx resistance gene have only been reported from South America. These Rx breaking isolates could potentially have an additional impact over the current situation in the EU and therefore meet all the criteria to qualify as a potential Union quarantine pest. All other non-EU isolates, should they be introduced, are not expected to have additional impact and therefore do not meet this criterion to qualify as a potential Union quarantine pest.

Plant diseases, including many plant viruses, are a continuous threat to the cost effective and s... more Plant diseases, including many plant viruses, are a continuous threat to the cost effective and safe production of food and cause significant losses in yield and quality of many important crops. It is therefore essential to minimise the impact of plant diseases through an effective and coordinated system of legislation, plant passports and testing laboratories. In such system, reliable and cost-effective diagnosis methods for plant viruses are essential. These only can be developed, validated and implemented when suitable reference materials are available. Historically, reference materials were supplied from collections maintained by European universities and research institutions. However the maintenance of such collections had come under severe pressure due to a decrease in the number of scientists (virologists in particular) and allocated budgets. For plant viruses and viroids, type isolates (if still available) were dispersed between different public and/or private collections (...

Nonsense-mediated mRNA decay (NMD) is a quality con-trol system that degrades mRNAs containing pr... more Nonsense-mediated mRNA decay (NMD) is a quality con-trol system that degrades mRNAs containing premature termination codons. Although NMD is well characterized in yeast and mammals, plant NMD is poorly understood. We have undertaken the functional dissection of NMD pathways in plants. Using an approach that allows rapid identification of plant NMD trans factors, we demonstrated that two plant NMD pathways coexist, one eliminates mRNAs with long 30UTRs, whereas a distinct pathway degrades mRNAs harbouring 30UTR-located introns. We showed that UPF1, UPF2 and SMG-7 are involved in both plant NMD pathways, whereas Mago and Y14 are required only for intron-based NMD. The molecular mechanism of long 30UTR-based plant NMD resembled yeast NMD, whereas the intron-based NMD was similar to mammalian NMD, suggesting that both pathways are evolutionarily conserved. Interestingly, the SMG-7 NMD component is targeted by NMD, suggesting that plant NMD is autoregu-lated. We propose that a complex, a...

The mechanisms by which Potato virus Y variants are generated and selected are still unclear. Spo... more The mechanisms by which Potato virus Y variants are generated and selected are still unclear. Spontaneous mutations generated by uncorrected replication error and recombination events between viral isolates during co-infection of plant cells are the main likely source of genetic diversity. This high level of diversity generation is essential for virus evolution and survival in different environments. Different PVY strain groups have appeared over time: firstly, non-recombinant PVYC, PVYO and PVYN strains and, more recently, recombinant PVYN-Wi and PVYNTN strains with novel biological characteristics and the ability to cause potato tuber necrotic ringspot disease (PTNRD). Increased fitness of the recombinant strains appears to have enabled them to replace the non-recombinant variants in most potato growing areas of the world. Partial sequencing of PVY genome (P1, HC-Pro, CP, recombinant junctions) and whole genome sequencing has shown that non-recombinant and recombinant variants are...

En reponse a une agression par un agent pathogene, les plantes developpent de nombreux mecanismes... more En reponse a une agression par un agent pathogene, les plantes developpent de nombreux mecanismes de defense. L'un d'entre eux est la reponse hypersensible (hr) reaction active de resistance, qui se caracterise par une mort cellulaire rapide, localisee au site d'inoculation. Afin d'identifier et de caracteriser des genes vegetaux actives precocement et specifiquement au cours de la hr, la strategie qui a ete developpee est basee sur le criblage differentiel d'une banque d'adnc construite a partir d'arnm isoles de suspensions cellulaires inoculees par l'isolat bacterien induisant la hr, en absence de synthese proteique. Cette approche a necessite la mise au point des conditions experimentales de l'interaction plante/pathogene en suspensions cellulaires et du traitement par un inhibiteur de la synthese proteique. Un sequencage systematique de la banque d'adnc, realise dans le cadre d'un projet national de sequencage du genome transcrit, a pe...

As obligate parasites, plant viruses, require in order to survive, to be transmitted to another p... more As obligate parasites, plant viruses, require in order to survive, to be transmitted to another plant. Experimentally, viruses such as Potato virus Y (PVY) can be transmitted by mechanical means such as wounding and grafting. In its natural environment, PVY transmission is mediated by sap-feeding aphid vector, or vegetatively through propagated organs such as potato tubers. A vast number of aphid species have been reported to transmit PVY in a non-persistent manner with variable efficiency to a large number of solanaceous and non-solanaceous plant species including weeds and ornamentals. Several sensory stimuli will influence host selection and feeding behaviour of the aphid and will strongly influence virus epidemiology. The interactions between the virus, its vector, and the environment are complex and are the focus of many studies aiming to understand the molecular basis of these interactions and their impact on disease development. This chapter will present the current knowledge...

EFSA Journal

Following a request from the EU Commission, the Panel on Plant Health has addressed the pest cate... more Following a request from the EU Commission, the Panel on Plant Health has addressed the pest categorisation of those viruses and viroids (hereafter referred to as viruses) of Solanum tuberosum and other tuber-forming Solanum spp. (hereafter referred to as potato) which are considered to be either non-EU or of undetermined standing based on a previous EFSA opinion. These viruses belong to different families and genera and either have an established identity or produce consistent symptoms. Plants for planting is the main pathway for entry for all categorised viruses as they can all be transmitted by vegetative propagation. Several categorised viruses have a relatively wide host range and/or are vector-transmitted, increasing the potential for entry. The information currently available on geographical distribution, biology, epidemiology, impact and potential entry pathways has been evaluated with regard to the criteria to qualify as potential Union quarantine pest or as Union regulated non-quarantine pest (RNQP). Since this opinion addresses specifically the non-EU potato viruses, in general these viruses do not meet the criteria assessed by EFSA to qualify as potential Union regulated non-quarantine pests. The following viruses meet the criteria to qualify as potential Union quarantine pest:

EFSA Journal

Following a request from the EU Commission, the Panel on Plant Health has addressed the pest cate... more Following a request from the EU Commission, the Panel on Plant Health has addressed the pest categorisation of non-EU isolates of potato virus M (PVM). The information currently available on geographical distribution, biology, epidemiology, potential entry pathways, potential additional impact compared to the current situation in the EU and availability of control measures of non-EU isolates of PVM has been evaluated with regard to the criteria to qualify as a potential Union quarantine pest. Because non-EU isolates of PVM are absent from the EU, they do not meet one of the requirements to be regulated as a regulated non-quarantine pest (RNQP) (presence in the EU); as a consequence, the Panel decided not to evaluate the other RNQP criteria for these isolates. Populations of PVM can be subdivided into two strains: the ordinary strain (PVM-O) is present in the EU, while the divergent strain (PVM-D) is absent from the EU or considered to have at most a limited distribution in the EU. Non-EU isolates of PVM-O are not expected to have an additional impact in the EU compared to EU isolates and therefore do not meet the corresponding criterion to qualify as a potential Union quarantine pest. The Panel is unable to conclude on the potential impact of non-EU PVM-D isolates in the EU territory, but PVM-D isolates meet all the other criteria to qualify as a potential Union quarantine pest.

Summary Barley stripe mosaic (BSMV) and potato mop-top virus (PMTV) genomes contain modules of th... more Summary Barley stripe mosaic (BSMV) and potato mop-top virus (PMTV) genomes contain modules of three overlapping genes called the triple gene block (TGB) of the hordeivirus type. The TGB proteins are essential for movement. In addition, BSMV encodes a multifunctional, cysteine rich protein called γB that has RNA silencing suppression and pathogenicity enhancing activities. Studies of the expression and localisation of fluorescent-protein tagged TGB2 proteins and γB using confocal microscopy have revealed that in addition to localisations in the ER, motile granules and at the cell periphery; later in expression, the TGB2 proteins associated with components of the endocytic pathway. Surprisingly, they also associated with plastids. Observations of thin sections of infected leaves suggested that plastids were sites of virus replication and the electron microscopy was confirmed by RT-PCR and Western blots of virus infected leaves and plastid preparations. The results suggest that the TG...

Potato virus Y: biodiversity, pathogenicity, epidemiology and management

Since the discovery of PVY in the 1930s, many strain groups and variants have been described alth... more Since the discovery of PVY in the 1930s, many strain groups and variants have been described although consensus on an agreed international nomenclature is still a matter of debate. The challenge for plant pathologists studying PVY remains to establish the biological significance of the genomic diversity of PVY arising from the new, diverse PVY populations and how it impacts on crop production in practice. The distribution and range of PVY variants identified over the years highlight the ongoing threat that PVY poses to solanaceous crops worldwide. While genome sequencing provides accurate information on the genomic structure of an isolate and has become the method of choice as a first step to studying the phylogeny of novel isolates and their affiliation to a genotypic group, it is not a sufficient criterion to assign a PVY isolate to a specific strain group, as groups are identified by a defined set of reactions or symptoms that develop following infection of a range of potato cultivars harbouring known resistance genes and on tobacco plants. The purpose of this chapter is to give an update on the current status of knowledge of PVY diversity identified in different geographical regions and insights into identification and classification of PVY variants.

Potato virus Y: biodiversity, pathogenicity, epidemiology and management

Achieving sustainable cultivation of potatoes Volume 2, 2018

The aim of the VirusCollect II project was to establish and extend an international network of co... more The aim of the VirusCollect II project was to establish and extend an international network of collections of plant viruses and viroids thereby making virus isolates available for reference at diagnostic and research laboratories in Plant Health. At present access to isolates of regulated viruses is limited and only the plant virus collection at DSMZ is officially accredited as reference producer. Strengthening the infrastructure of plant virus collections is required because diagnostic tests on regulated organisms have to be accredited under the new Plant Health rules of the European Union that apply from December 14^th 2019. The ability of laboratories of National Plant Protection Organizations (NPPOs) to fulfil this requirement will depend on public access to well-characterised virus isolates. The collaboration between partners of the Euphresco projects NGS-detect and VirusCollect II and especially their joint meetings offered a fruitful platform for exchang...

The worldwide prevalence of Potato virus Y (PVY) poses a continuous challenge to efficient potato... more The worldwide prevalence of Potato virus Y (PVY) poses a continuous challenge to efficient potato production. The accurate diagnosis of viruses such as PVY is inherently challenging due to the broad biological and genetic diversity of PVY strains that elicit a range of symptoms and diseases in various potato cultivars and related solanaceous species. A wide range of techniques have been developed over a period of 50 years for the detection of PVY. Serological methods such as ELISA, using polyclonal and especially monoclonal antibodies, have been widely used by most diagnostic laboratories, due to their cost effectiveness and capacity to implement for a large number of samples. Over the last decade, PCR-based assays have been routinely used in diagnostic laboratories because of their sensitivity, specificity and their capacity to be automated for high-throughput testing. The objective of this chapter is to provide a brief historical overview of the main diagnostic methods used to det...

Diseases caused by plant viruses can have significant and devastating impacts on many cultivated ... more Diseases caused by plant viruses can have significant and devastating impacts on many cultivated crops worldwide. The impact of disease caused by a virus depends on the virus species, strains, type of inoculum, host plant characteristics, vector pressure, climatic conditions, trade, changes in agricultural landscape and intensive production practices. Viruses affect plants by causing a large variety of symptoms such as alteration of shape, pigmentation, necrosis on different parts of the plant, thus affecting plant development. In most of the cases, these lead to a decrease in crop yield and quality. There are numerous viruses that affect potato; among them, Potato virus Y is considered to be one of the ten most important plant viruses of crops, because of its worldwide distribution and economic impact. Some PVY isolates are able to cause potato ringspot necrotic disease in infected tubers rendering them unmarketable. Understanding the genetic diversity and molecular biology of PVY ...

RSC Chemical Biology, 2020

A novel DNA sensing method based on LD spectroscopy and using bionanoparticle scaffolds is descri... more A novel DNA sensing method based on LD spectroscopy and using bionanoparticle scaffolds is described, as demonstrated by the rapid detection of DNA strands associated with bacterial and viral pathogens.

Methods in Molecular Biology, 2015

EFSA Journal, 2020

Following a request from the EU Commission, the Panel on Plant Health has addressed the pest cate... more Following a request from the EU Commission, the Panel on Plant Health has addressed the pest categorisation of non-EU isolates of potato virus X (PVX). The information currently available on geographical distribution, biology, epidemiology, potential entry pathways, potential additional impact and availability of control measures of non-EU isolates of PVX has been evaluated with regard to the criteria to qualify as a potential Union quarantine pest. Because non-EU isolates of PVX are absent from the EU, they do not meet one of the requirements to be regulated as a regulated non-quarantine pest (RNQP) (presence in the EU); as a consequence, the Panel decided not to evaluate the other RNQP criteria for these isolates. On the basis of their ability to overcome potato resistance genes, PVX isolates can be divided into several pathotypes. PVX isolates that are not able to overcome resistance genes and PVX isolates that are able to overcome the Nb and/or Nx resistance genes are already present in the EU. Isolates able to overcome the Rx resistance gene have only been reported from South America. These Rx breaking isolates could potentially have an additional impact over the current situation in the EU and therefore meet all the criteria to qualify as a potential Union quarantine pest. All other non-EU isolates, should they be introduced, are not expected to have additional impact and therefore do not meet this criterion to qualify as a potential Union quarantine pest.

Plant diseases, including many plant viruses, are a continuous threat to the cost effective and s... more Plant diseases, including many plant viruses, are a continuous threat to the cost effective and safe production of food and cause significant losses in yield and quality of many important crops. It is therefore essential to minimise the impact of plant diseases through an effective and coordinated system of legislation, plant passports and testing laboratories. In such system, reliable and cost-effective diagnosis methods for plant viruses are essential. These only can be developed, validated and implemented when suitable reference materials are available. Historically, reference materials were supplied from collections maintained by European universities and research institutions. However the maintenance of such collections had come under severe pressure due to a decrease in the number of scientists (virologists in particular) and allocated budgets. For plant viruses and viroids, type isolates (if still available) were dispersed between different public and/or private collections (...

Nonsense-mediated mRNA decay (NMD) is a quality con-trol system that degrades mRNAs containing pr... more Nonsense-mediated mRNA decay (NMD) is a quality con-trol system that degrades mRNAs containing premature termination codons. Although NMD is well characterized in yeast and mammals, plant NMD is poorly understood. We have undertaken the functional dissection of NMD pathways in plants. Using an approach that allows rapid identification of plant NMD trans factors, we demonstrated that two plant NMD pathways coexist, one eliminates mRNAs with long 30UTRs, whereas a distinct pathway degrades mRNAs harbouring 30UTR-located introns. We showed that UPF1, UPF2 and SMG-7 are involved in both plant NMD pathways, whereas Mago and Y14 are required only for intron-based NMD. The molecular mechanism of long 30UTR-based plant NMD resembled yeast NMD, whereas the intron-based NMD was similar to mammalian NMD, suggesting that both pathways are evolutionarily conserved. Interestingly, the SMG-7 NMD component is targeted by NMD, suggesting that plant NMD is autoregu-lated. We propose that a complex, a...

The mechanisms by which Potato virus Y variants are generated and selected are still unclear. Spo... more The mechanisms by which Potato virus Y variants are generated and selected are still unclear. Spontaneous mutations generated by uncorrected replication error and recombination events between viral isolates during co-infection of plant cells are the main likely source of genetic diversity. This high level of diversity generation is essential for virus evolution and survival in different environments. Different PVY strain groups have appeared over time: firstly, non-recombinant PVYC, PVYO and PVYN strains and, more recently, recombinant PVYN-Wi and PVYNTN strains with novel biological characteristics and the ability to cause potato tuber necrotic ringspot disease (PTNRD). Increased fitness of the recombinant strains appears to have enabled them to replace the non-recombinant variants in most potato growing areas of the world. Partial sequencing of PVY genome (P1, HC-Pro, CP, recombinant junctions) and whole genome sequencing has shown that non-recombinant and recombinant variants are...

En reponse a une agression par un agent pathogene, les plantes developpent de nombreux mecanismes... more En reponse a une agression par un agent pathogene, les plantes developpent de nombreux mecanismes de defense. L'un d'entre eux est la reponse hypersensible (hr) reaction active de resistance, qui se caracterise par une mort cellulaire rapide, localisee au site d'inoculation. Afin d'identifier et de caracteriser des genes vegetaux actives precocement et specifiquement au cours de la hr, la strategie qui a ete developpee est basee sur le criblage differentiel d'une banque d'adnc construite a partir d'arnm isoles de suspensions cellulaires inoculees par l'isolat bacterien induisant la hr, en absence de synthese proteique. Cette approche a necessite la mise au point des conditions experimentales de l'interaction plante/pathogene en suspensions cellulaires et du traitement par un inhibiteur de la synthese proteique. Un sequencage systematique de la banque d'adnc, realise dans le cadre d'un projet national de sequencage du genome transcrit, a pe...

As obligate parasites, plant viruses, require in order to survive, to be transmitted to another p... more As obligate parasites, plant viruses, require in order to survive, to be transmitted to another plant. Experimentally, viruses such as Potato virus Y (PVY) can be transmitted by mechanical means such as wounding and grafting. In its natural environment, PVY transmission is mediated by sap-feeding aphid vector, or vegetatively through propagated organs such as potato tubers. A vast number of aphid species have been reported to transmit PVY in a non-persistent manner with variable efficiency to a large number of solanaceous and non-solanaceous plant species including weeds and ornamentals. Several sensory stimuli will influence host selection and feeding behaviour of the aphid and will strongly influence virus epidemiology. The interactions between the virus, its vector, and the environment are complex and are the focus of many studies aiming to understand the molecular basis of these interactions and their impact on disease development. This chapter will present the current knowledge...

EFSA Journal

Following a request from the EU Commission, the Panel on Plant Health has addressed the pest cate... more Following a request from the EU Commission, the Panel on Plant Health has addressed the pest categorisation of those viruses and viroids (hereafter referred to as viruses) of Solanum tuberosum and other tuber-forming Solanum spp. (hereafter referred to as potato) which are considered to be either non-EU or of undetermined standing based on a previous EFSA opinion. These viruses belong to different families and genera and either have an established identity or produce consistent symptoms. Plants for planting is the main pathway for entry for all categorised viruses as they can all be transmitted by vegetative propagation. Several categorised viruses have a relatively wide host range and/or are vector-transmitted, increasing the potential for entry. The information currently available on geographical distribution, biology, epidemiology, impact and potential entry pathways has been evaluated with regard to the criteria to qualify as potential Union quarantine pest or as Union regulated non-quarantine pest (RNQP). Since this opinion addresses specifically the non-EU potato viruses, in general these viruses do not meet the criteria assessed by EFSA to qualify as potential Union regulated non-quarantine pests. The following viruses meet the criteria to qualify as potential Union quarantine pest:

EFSA Journal

Following a request from the EU Commission, the Panel on Plant Health has addressed the pest cate... more Following a request from the EU Commission, the Panel on Plant Health has addressed the pest categorisation of non-EU isolates of potato virus M (PVM). The information currently available on geographical distribution, biology, epidemiology, potential entry pathways, potential additional impact compared to the current situation in the EU and availability of control measures of non-EU isolates of PVM has been evaluated with regard to the criteria to qualify as a potential Union quarantine pest. Because non-EU isolates of PVM are absent from the EU, they do not meet one of the requirements to be regulated as a regulated non-quarantine pest (RNQP) (presence in the EU); as a consequence, the Panel decided not to evaluate the other RNQP criteria for these isolates. Populations of PVM can be subdivided into two strains: the ordinary strain (PVM-O) is present in the EU, while the divergent strain (PVM-D) is absent from the EU or considered to have at most a limited distribution in the EU. Non-EU isolates of PVM-O are not expected to have an additional impact in the EU compared to EU isolates and therefore do not meet the corresponding criterion to qualify as a potential Union quarantine pest. The Panel is unable to conclude on the potential impact of non-EU PVM-D isolates in the EU territory, but PVM-D isolates meet all the other criteria to qualify as a potential Union quarantine pest.

Summary Barley stripe mosaic (BSMV) and potato mop-top virus (PMTV) genomes contain modules of th... more Summary Barley stripe mosaic (BSMV) and potato mop-top virus (PMTV) genomes contain modules of three overlapping genes called the triple gene block (TGB) of the hordeivirus type. The TGB proteins are essential for movement. In addition, BSMV encodes a multifunctional, cysteine rich protein called γB that has RNA silencing suppression and pathogenicity enhancing activities. Studies of the expression and localisation of fluorescent-protein tagged TGB2 proteins and γB using confocal microscopy have revealed that in addition to localisations in the ER, motile granules and at the cell periphery; later in expression, the TGB2 proteins associated with components of the endocytic pathway. Surprisingly, they also associated with plastids. Observations of thin sections of infected leaves suggested that plastids were sites of virus replication and the electron microscopy was confirmed by RT-PCR and Western blots of virus infected leaves and plastid preparations. The results suggest that the TG...

Potato virus Y: biodiversity, pathogenicity, epidemiology and management

Since the discovery of PVY in the 1930s, many strain groups and variants have been described alth... more Since the discovery of PVY in the 1930s, many strain groups and variants have been described although consensus on an agreed international nomenclature is still a matter of debate. The challenge for plant pathologists studying PVY remains to establish the biological significance of the genomic diversity of PVY arising from the new, diverse PVY populations and how it impacts on crop production in practice. The distribution and range of PVY variants identified over the years highlight the ongoing threat that PVY poses to solanaceous crops worldwide. While genome sequencing provides accurate information on the genomic structure of an isolate and has become the method of choice as a first step to studying the phylogeny of novel isolates and their affiliation to a genotypic group, it is not a sufficient criterion to assign a PVY isolate to a specific strain group, as groups are identified by a defined set of reactions or symptoms that develop following infection of a range of potato cultivars harbouring known resistance genes and on tobacco plants. The purpose of this chapter is to give an update on the current status of knowledge of PVY diversity identified in different geographical regions and insights into identification and classification of PVY variants.

Potato virus Y: biodiversity, pathogenicity, epidemiology and management