Archive for the ‘Viruses’ Category

New research shows gene exchange between viruses and hosts drives evolution

Date:January 5, 2022Source:University of British ColumbiaSummary:The first comprehensive analysis of viral horizontal gene transfer (HGT) illustrates the extent to which viruses pick up genes from their hosts to hone their infection process, while at the same time hosts also co-opt useful viral genes.Share:FULL STORY

Viruses illustration (stock image).Credit: © successphoto / stock.adobe.com

The first comprehensive analysis of viral horizontal gene transfer (HGT) illustrates the extent to which viruses pick up genes from their hosts to hone their infection process, while at the same time hosts also co-opt useful viral genes.

HGT is the movement of genetic material between disparate groups of organisms, rather than by the “vertical” transmission of DNA from parent to offspring. Previous studies have looked at HGT between bacteria and their viruses and have shown that it plays a major role in the movement of genes between bacterial species. However the new study, published in Nature Microbiology, looks at interactions between viruses and eukaryotes, which include animals, plants, fungi, protists and most algae.

“We knew from individual examples that viral genes have played a role in the evolution of eukaryotes. Even humans have viral genes, which are important for our development and brain function,” said the study’s lead author, Dr. Nicholas Irwin, a Junior Research Fellow at Merton College, University of Oxford, and former PhD student at the University of British Columbia (UBC). “We wanted to understand more broadly how HGT has affected viruses and eukaryotes from across the tree of life.”

To tackle this problem, the authors examined viral-eukaryotic gene transfer in the genomes of hundreds of eukaryotic species and thousands of viruses. They identified many genes that had been transferred and found that HGT from eukaryotes to viruses was twice as frequent as the reverse direction.

“We were interested to find that certain groups of viruses, especially those that infect single-celled eukaryotes, acquire a lot of genes from their hosts,” said the study’s senior author, Dr. Patrick Keeling, a professor in the Department of Botany at UBC. “By studying the function of these genes we were able to make predictions about how these viruses affect their hosts during infection.”

In contrast to viruses, eukaryotic organisms retained fewer viral genes, although the ones that were kept appear to have had a major impact on host biology over evolutionary time.

“Many of these viral-derived genes appear to have repeatedly affected the structure and form of different organisms, from the cell walls of algae to the tissues of animals,” said Dr. Irwin. “This suggests that host-virus interactions may have played an important role in driving the diversity of life we see today.”

“These transfers not only have evolutionary consequences for both virus and host, but could have important health implications,” Dr. Keeling said.

HGT allows genes to jump between species including viruses and their hosts. If the gene does something useful, it can sweep through the population and become a feature of that species. This can lead to a rapid emergence of new abilities, as opposed to the more incremental changes that result from smaller mutations.

Although viruses such as Zika and coronaviruses do not appear to participate in these gene transfers, they often manipulate similar genes in their hosts through complex mechanisms. Future research into these transferred genes may therefore provide a novel approach for understanding the infection processes of these and other viruses which could be important for drug discovery.

“The past two years have clearly demonstrated the destructive potential of viruses, but we think that this work serves as an interesting reminder that viruses have also contributed to the evolution of life on Earth,” said Dr. Irwin.

Story Source:

Materials provided by University of British ColumbiaNote: Content may be edited for style and length.

Journal Reference:

  1. Nicholas A. T. Irwin, Alexandros A. Pittis, Thomas A. Richards, Patrick J. Keeling. Systematic evaluation of horizontal gene transfer between eukaryotes and virusesNature Microbiology, 2021; DOI: 10.1038/s41564-021-01026-3

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New focus on emerging viral diseases

November 09, 2021

A new Horizon 2020 project is underway to address viral diseases responsible for major crop losses in tomatoes and cucurbits in Europe and beyond. Called ‘VIRTIGATION – Emerging viral diseases in tomatoes and cucurbits: Implementation of mitigation strategies for durable disease management’, the project includes INRAE, one of ENDURE’s French partners, Germany’s Julius Kühn Institute (JKI) and Wageningen University (WU) and Stichting Wageningen Research (WR) from the Netherlands.

VIRTIGATION is running for four years (2021 to 2025) and is being coordinated by the Laboratory for Tropical Crop Improvement at the Department of Biosystems of KU Leuven (Belgium). In particular, it is seeking to develop short, medium and long-term solutions to whitefly-transmitted begomoviruses and mechanically transmitted tobamoviruses in tomato and cucurbit crops.

The project reports: “Every year, viral diseases wreak havoc on tomato and cucurbit crops worldwide, destroying in Europe alone billions of EUR in harvest. The EU-funded VIRTIGATION project is on a mission to combat this viral crop destruction and safeguard tomatoes and cucurbits.

“Viral diseases are not only affecting European fields and greenhouses: across the globe, from Morocco, Israel to India, tomatoes and cucurbits are vital staple crops that are under threat. Colossal losses in harvests have been reported, ranging from 15% to entire crop destruction. As the world needs to increase its food production by at least half by 2050 to feed a growing population, mitigating the devastating impact of plant diseases is essential to ensure sufficient food supply, both in quantity and quality.”

VIRTIGATION has set itself six specific objectives:

  • Knowledge sharing and engagement of stakeholders in research activities
  • Develop robust diagnostic tests, quarantine measures and identify ecological factors driving disease outbreaks
  • Understand plant-virus-vector interactions
  • Develop IPM solutions
  • Identify and pyramid natural resistance to viral diseases and vectors
  • Train the tomato and cucurbit value chains

INRAE will be involved in the research on viral genome sequencing and monitoring virus outbreaks, plant-virus-vector interactions and the spread of emerging viral diseases under climate change, and will also be the National Knowledge Broker for France in the project’s multi-actor approach.

JKI is the National Knowledge Broker for Germany and will mainly be involved in the “research on plant-virus-vector interactions and integrated virus and vector management, where it is exploring viral symptom determinants of ToBRFV (Tomato brown rugose fruit virus) to support the search for virus isolates that could be used in cross-protection strategies”.

WU will be contributing to the research on plant-virus-vector interactions and the spread of emerging viral diseases under climate change, with a focus on tomato-geminivirus-whitefly interactions, and finding tomato genes for resistance to ToBRFV.

WR’s departments of Plant Breeding and Biointeractions & Plant Health are contributing to all the project’s research work packages, “with a particular focus on virus epidemiology and ecology, as well as virus and vector control through breeding and Integrated Pest Management (IPM)”. WR is also the National Knowledge Broker for the Netherlands.

For more information:

Last update: 23/12/2021 – ENDURE © 2009 – 

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Jörg Eggers (Europlant Ltd) on today’s potato market

“We have a number of virus-resistant variety candidates in the pipeline”

On December 7, the internationally operating potato breeder Europlant Ltd invited interested parties to the Online Forum or Potato Day 2021. Europlant CEO Jörg Eggers first looked back on the past cultivation and harvest year. As expected, there was a reduction in yields last season, especially for table potatoes. In addition, there was a very late spring with planting until mid-June, which meant that the planting dates were often no longer optimal. Furthermore, late crop development and in some cases very low tuber set were observed.

At the beginning, the external quality of the potatoes was acceptable to good, but due to weather conditions and very late harvest dates, there were more defects later on. “For seed and ware potatoes, there will be below-average net quantities this year. The same applies to the typical recipient countries of German table potatoes in Central and Eastern Europe and Southeastern Europe. The quality after storage will be decisive, also for the subsequent price development of the potatoes,” Eggers explains.

Jörg Eggers delved into several topics related to potato cultivation and marketing.

‘Table potatoes could become scarce’
European potato acreage is trending downward: “If demand for fries returns to normal and the planned expansions in the processing sector become a fact, table potatoes could become scarce in the coming years, unless cultivation becomes more interesting compared to other crops,” Eggers added. According to the Europlant boss, there will be several challenges for the German potato sector in the near future, such as the restriction of plant treatment products, severe weather events, the problems with root penetration and the associated longer crop rotation and – last but not least – the higher consumer expectation in terms of quality, while the possibilities in production can rather be described as limited.

From today’s perspective, the Mediterranean countries will keep their area of early table potatoes stable, while southeastern Europe will generally continue to restrict their acreages, with a corresponding increase in demand. In Central and Eastern Europe, a slight expansion of cultivation is expected, with a steady demand nevertheless. In northwestern Europe, the area under ware potatoes is expected to stabilize, Eggers predicts, provided that the pandemic not lead to further restaurant closures.

Resistant varieties
Following the outlook and forecasts, Eggers answered several questions from online participants. For example, there were specific questions about breeding disease-resistant varieties. Eggers commented, “With certain varieties, we already bring high recognition reliability and virus resistance. If we wanted to combine the great traits and qualities of our varieties with resistance, the breeding process would be much more complex. We have a number of candidate varieties in the pipeline that can take this position in the coming years.”

Organic table potatoes
The rapidly expanding cultivation of organic potatoes was also addressed. “In my view, production must be based on demand. There is no point and no purpose if we were to produce organic potatoes on 20 to 30 percent of the German cultivated area. That is not for sale. The share of organic table potatoes in total sales is currently around 8-10 percent and roughly corresponds to the multiplication area we currently have. I do not expect organic table potatoes to come from abroad on a large scale, especially since the EU organic regulation is a basic requirement there as well. Something will come from Spain, Italy and other early countries. Otherwise, in my view, there is a lack of purchasing power and production security,” Eggers said.

For more information:
Europlant GmbH
Jörg EggersWulf-Werum-Straße 1
21337 Lüneburg
Tel +49 4131 7480-05
Fax +49 4131 7480-580

Publication date: Fri 10 Dec 2021

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“What we saw convinced us again that the ToBRFV resistance is holding very well”

In October 2020, Enza Zaden announced the discovery of the High Resistance gene to ToBRFV. The one and only solution to beat this devastating tomato virus.

Fast forward to today, one year later: what has happened in the past year? Where are we now? And what is yet to come? 

Martijn van Stee, Crop Breeding Manager Tomato, gives an insight into the process to create high-resistant varieties: “Since we discovered the ToBRFV high resistance gene we worked hard on introducing it in our elite parent lines. At this moment we have high-quality parent lines with the ToBRFV resistance. This helps us to make high resistance tomato varieties.”  

Check out the video here.

Trials confirm high resistance 
Besides working on the parent lines, Enza Zaden has done some extensive trials with high resistant varieties in the past year. Martijn: “We trialed the first tomato varieties already in Europe, Mexico, and the Middle East. And what we saw there really convinced us again that the ToBRFV resistance is holding very well.” 

Kees Konst, Crop Research Director, continues: “In the meantime, we started up also the seed production of the hybrids. We already have some examples of high resistance varieties in our hands.” 

Importance of high resistance to ToBRFV 
The gene that Enza Zaden has discovered provides high resistance to ToBRFV. Kees explains the importance of high resistance. “With high resistance, you will not have any problems, because there is no virus in the plant or the fruit. You keep your soil, your water, everything clean.” 

What’s next? 
Eradicating the virus remains our top priority. This is something we can only achieve together with the growers and the fresh produce industry. Martijn: “Our breeders are very busy filling the pipeline. To make more elite parent lines with resistance, to make more varieties with resistance. The solution is right around the corner.”\For more informationEnza Zaden

Publication date: Wed 1 Dec 2021

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Massimo Pavan

Italy: “The summer season was a disaster due to the high temperatures and diseases”

Table tomatoes represent the most valuable vegetable and are among the most important consumer products. Massimo Pavan, an Italian expert and vice-president of Consorzio di Tutela del Pomodoro di Pachino Igp, explains how the summer was a disaster for growers. 

Now that the summer season has ended, the time has come for a winter season with table tomatoes grown in greenhouses in the Mediterranean areas, with Sicily standing out thanks to its prestigious productions.

“The summer season was a disaster due to the high temperatures and diseases. Although Tuta absoluta did not cause much trouble as it was exterminated by the high temperatures, there were other threats such as the Tomato Brown Rugose Fruit Virus. The drought that hit Sicily caused a 50% drop in production, leading to doubled production costs.”

“Although prices were rather high during the period in question, the favorable quotations were not enough to repay the losses in absolute terms. Cherry tomatoes, with peaks of over €2/kg, settled at an average of €1.50/kg. Thus, we were not pleased with the summer of 2021, especially considering the continuous price increases of the raw materials. Prices have increased so quickly that it is difficult to quantify the actual cost index. In addition, the cost of energy and fuel has also increased in October, which affected November production.”

“The prices are currently low, as is demand in foreign markets such as Germany and Austria. Production prices hover between €0.80 and €1.20/kg with considerable Moroccan competition in the European markets. We know November is traditionally a calmer month, but this month there is a lack of consumer trust, probably due to the uncertainty caused by Covid. In addition, they are starting to be affected by the higher cost of living. Because of that, producers are not seeing increases in sales. We are currently reaching the break-even point at €1.30/kg. We are talking about presumed indexes because the situation is still unclear. After all, assessments must be made at the end of the season. Anyway, we are working at a loss below this threshold, while last year production prices were €1.10/kg.”

“What seems to be happening is a reduction of the cultivation areas destined for tomatoes, which is what occurred in Spain. It will be a physiological consequence of a trend that is difficult to manage. Competition deals with quality, and ours is unbeatable. However, the Maghreb produce has lower prices. The reasons for this difference are well known, starting with the defense tools used in Morocco, which guarantee higher yields. Another determining factor is the cost of labor which, in the north-African country, is 8 times lower than in Italy.”

“Initiatives such as that promoted by Consorzio di Tutela del Pomodoro di Pachino Igp are welcome, as they focus on the sustainability of the product as a promotional strategy. Consumers have the certainty of purchasing a product that is monitored, healthy, and with an excellent flavor, and they can count on a carbon footprint that is exceptionally low, as greenhouses are not heated and do not release CO2 into the atmosphere, unlike what happens in northern Italy and Europe.”

Publication date: Wed 1 Dec 2021

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Kenyan scientist warns for impact ToBRFV on African growers

Tomato farmers in Africa have been urged to be on the lookout for the ToBRFV virus that has been causing havoc in most tomato-growing countries. Speaking during African Seed Trade Association (AFSTA) Congress in September this year, Dr. Isaac Macharia, General Manager, Phytosanitary Services at the Kenya Plant Health Inspectorate Service (KEPHIS), said countries in Africa are encouraged to report the occurrence of the disease to ensure other countries prepare.

“This virus is more severe on young tomato plants and can result in 30-70% yield loss. The unique thing about this virus is that it doesn’t infect the embryo of the seed but instead contaminates the seed coat,” he added. “Its rapid spread demonstrates that ToBRFV has become a worldwide threat to tomato production. The continent needs to prepare for the negative impact of the disease in tomato production,” he said.

“There is a need to ensure we prevent the introduction of this virus in most of our countries. We can achieve that if we embrace pre-shipment testing of all imported tomato, capsicum, and eggplant seeds, regardless of their origin, using an appropriate method such as real-time Polymerase Chain Reaction,” he said. He added that there was a need to sensitize importers of tomato/capsicum seed and commercial growers to ensure early reporting of cases.

Breeders also need to work towards the development of varieties with durable resistance genes since phylogenetic analysis shows the genomic sequence of ToBRFV differs from both ToMV and TMV.  “There is also need to invest in laboratory diagnosis for diseases, including tomato diseases. This will help countries carry out continuous tests for a proportion of seed and seedlings for ToBRFV,” he added.

Since Kenya imports most tomato, capsicum, and eggplant seeds from different countries, including those where ToBFRV has been reported, Macharia says it is now mandatory for all imported tomato seeds to be tested using real-time PCR. So far, about 192 imported seeds lots have been tested since February 2021, and no positive samples have been registered so far.

A field survey was also done in 2019 and 256 leaf samples were analyzed (245 tomatoes, 10 capsicums, 1 black nightshade) and all samples tested negative. Despite the negative results, emergency measure on ToBRFV was issued to all-out trading partners and import conditions for tomato and capsicum were amended to include pre-shipment testing and upon importation. 

“We will continue to conduct continuous surveillance to ensure this virus doesn’t get to our country. We are also going to develop contingency plans to prevent spread in case of introduction,” reveals Macharia.

Read the complete article at www.standardmedia.co.ke

Publication date: Wed 17 Nov 2021

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ToBRFV in Saudia Arabia & Iran

In Iran, symptoms resembling those of tomato brown rugose fruit virus were first observed in August 2021 in tomato plants (Solanum lycopersicum) grown in a greenhouse in Isfahan province. The plants had been grown from imported seed. The identity of the virus was confirmed by RT-PCR. All plants were removed and destroyed

In Saudi Arabia, symptoms resembling those of tomato brown rugose fruit virus (Tobamovirus, ToBRFV – EPPO A2 List) were first observed in January 2021 in tomato plants (Solanum lycopersicum) grown in several greenhouses in Riyadh region. The identity of the virus was confirmed by RT-PCR and partial nucleotide sequence. ToBRFV was identified in 25 out of 45 samples taken (Sabra et al., 2021).

Source: EPPO

Publication date: Mon 29 Nov 2021

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BBTD Alliance continues to tackle banana bunchy top disease in Africa

Up to 16 African countries have now experienced the banana bunchy top disease (BBTD), caused by the banana bunchy top virus. The virus is also endangering the diversity of banana varieties grown by these farmers. The CGIAR Research Program on Roots, Tubers and Bananas (RTB) is combating the virus through the Alliance for Banana Bunchy Top Disease Control in Africa.

The BBTD Alliance convened international, multi-stakeholder teams fostering cutting-edge research for development (R4D) to establish practical solutions so farmers can once again produce bananas for food and income. The Alliance has collaborated with national programs, building their capacity to detect, surveil, and control BBTD.

The BBTD Alliance develops new knowledge and management technologies, facilitates training and information exchange, and supports national partners and farmer organizations. Seed entrepreneurs, extension agents, farmers, and plant health inspectors are learning to diagnose the disease in the field, identify rogue infected plants, and produce clean planting material. In 2020, RTB developed an online training course on disease recognition and eradication.

Source: iita.org

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Researchers develop new method to quickly diagnose bean viruses

Lim Chang-won Reporter(cwlim34@ajunews.com) | Posted : November 10, 2021, 08:30 | Updated : November 10, 2021, 08:30

[Courtesy of Gyeonggido Business & Science Accelerator]
SEOUL — Soybean virus diseases result in reduced yields and inferior quality. Polymerase chain reaction (PCR), a method used in molecular biology, has been widely used to diagnose bean viruses, but it takes up to two weeks to acquire results. South Korean researchers have developed an envelope protein screening method that can easily identify bean viruses.

The common mosaic virus is seed-borne and causes mosaic and lesions on foliage as well as blackened roots. The yellow mosaic virus is often associated with the presence of virus source plants, with symptoms consisting of leaf mosaic formed by contrasting yellow or green mosaic areas.

After dropping a sample collected by scratching the skin of a bean into the diagnostic kit, it will be possible to check the results in five minutes. It enabled the selection of mini antibody candidates without a protein purification process, the bio-center of Gyeonggido Business & Science Accelerator (GBSA) said, adding the commercialization of diagnostic devices based on GBSA’s technology would replace imports.

The center said its research team proposed a new platform for the production of plant virus diagnostic kits using the combined module of SpyTag (peptide) and SpyCatcher (protein) for the binding of antigens and coat proteins. Using SpyTag and SpyCatcher, bioconjugation can be achieved between two recombinant proteins that would otherwise be restrictive or impossible with the traditional direct genetic fusion between the two proteins.

“Through continuous research and development, it has become possible to diagnose the virus in the early stages and preemptively block it,” an unnamed GBSA official said in a statement. “We will contribute to stable agricultural production by reducing economic losses caused by crop virus damage.” The study was conducted jointly with researchers from Kyungpook National University, the Rural Development Administration and the Ajou University College of Medicine.

Lim Chang-won ReporterLim Chang-won Reporteremail : cwlim34@ajunews.com© Aju Business Daily & http://www.ajunews.com Copyright: All materials on this site may not be reproduced, distributed, transmitted, displayed, published or broadcast without the authorization from the Aju News Corporation.

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Tomato exports to eight countries still off the table due to plant disease

8:32 pm on 28 October 2021 Share this 

RNZ New Zealand

It’s peak tomato season but exports to eight countries remain off the table after the discovery of a plant disease here.No caption

Photo: Thomas Martinsen/ Unsplash

In April, Pepino Mosaic Virus was found in a greenhouse in Auckland. The extremely contagious disease can affect the yield of crops and delay fruit growth.

The Ministry for Primary Industries said following the initial detection, the virus had since spread to four more glasshouses.

Exports have been put on ice for eight countries where the disease is a biosecurity concern, including Australia and some Pacific nations.

Tomatoes NZ general manager Helen Barnes said while its biggest market, Japan, was still open for business, the situation was not ideal given Covid-related freight problems were already testing growers.

“There’s a bit of uncertainty and it’s quite challenging.”

Barnes said because the virus had only been on the industry’s radar for six months it was unclear what impact it would have on New Zealand’s tomato crops.

“It seems to be that if you’ve got a strong healthy crop, then the plants seem to grow through the virus. We’re still learning a lot.”

The Ministry for Primary Industries is working to reopen several export markets for tomato growers as they approach the peak of the export period.

MPI biosecurity response manager David Yard said it was providing assurances to these markets about the efforts going into controlling the disease.

“We’re working with the industry now on improving good biosecurity, keeping things clean, controlling people movements, and disposing of green waste, to try and minimise the spread of this virus to further greenhouse complexes.”

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Natural resources resistance to tomato spotted wilt virus

Tomato spotted wilt virus (TSWV) is one of the most destructive diseases affecting tomato (Solanum lycopersicum) cultivation and production worldwide. As defenses against TSWV, natural resistance genes have been identified in tomatoes, including Sw-1a, Sw-1b, sw-2, sw-3, sw-4, Sw-5, Sw-6, and Sw-7.

However, only Sw-5 exhibits a high level of resistance to the TSWV. Thus, it has been cloned and widely used in the breeding of tomatoes with resistance to the disease. Due to the global spread of TSWV, resistance induced by Sw-5 decreases over time and can be overcome or broken by a high concentration of TSWV. How to utilize other resistance genes and identify novel resistance resources are key approaches for breeding tomatoes with resistance to TSWV.

In this review, the characteristics of natural resistance genes, natural resistance resources, molecular markers for assisted selection, and methods for evaluating resistance to TSWV are summarized. The aim is to provide a theoretical basis for identifying, utilizing resistance genes, and developing tomato varieties that are resistant to TSWV.

Read the complete research at www.researchgate.net.

Qi, Shiming & Zhang, Shijie & Islam, Md & El-Sappah, Ahmed & Liang, Yan. (2021). Natural Resources Resistance to Tomato Spotted Wilt Virus (TSWV) in Tomato (Solanum lycopersicum). International Journal of Molecular Sciences. 22. 10.3390/ijms222010978. 

Publication date: Tue 19 Oct 2021

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