Revealing new information from existing genomic data for pepper mild mottle virus pathotype determination

Đeri, Bojana Banović; Pajić, Vesna; Dudić, Dragana

doi:10.1016/j.cropro.2018.01.017

Cited by 4 publications

(7 citation statements)

References 38 publications

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“…Belonging to the Virgaviridae family and Tobamovirus genus, this pepper plant pathogen is transmitted via mechanical contact with contaminated soil and/or seed and causes fruit malformation and leaf mosaic in Capsicum species throughout Asia, Australia, Europe, Middle East, and North and South America (Adkins et al, 2001, Ahmad et al, 2015, Alonso et al, 1991, Beczner et al, 1997, Çağlar et al, 2013, Garcia-Luque et al, 1993, Genda et al, 2007, Han et al, 2017, Ichiki et al, 2009, Kaur et al, 2014, Milošević et al, 2015, Oliveira et al, 2010, Wang et al, 2006, Wetter et al, 1984, Yu et al, 2018). PMMoV has a 6,356 bp genome that encodes for a capsid, two replication-associated proteins (126 kDa and 183 kDa), and a cell-to-cell movement-associated protein (Banović Đeri et al, 2018, Oliveira et al, 2010). Given the limited genetic variability of PMMoV, it has been suggested that the PMMoV genome is highly stable (Rodriguez-Cerezo et al, 1989) and limited sequence variation has been observed among geographic regions (Yu et al, 2018).…”

Section: Pepper Mild Mottle Virus Ecology and Its Origin In Human Fecesmentioning

confidence: 99%

Pepper mild mottle virus: A plant pathogen with a greater purpose in (waste)water treatment development and public health management

et al. 2018

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An enteric virus surrogate and reliable domestic wastewater tracer is needed to manage microbial quality of food and water as (waste)water reuse becomes more prevalent in response to population growth, urbanization, and climate change. Pepper mild mottle virus (PMMoV), a plant pathogen found at high concentrations in domestic wastewater, is a promising surrogate for enteric viruses that has been incorporated into over 29 water- and food-related microbial quality and technology investigations around the world. This review consolidates the available literature from across disciplines to provide guidance on the utility of PMMoV as either an enteric virus surrogate and/or domestic wastewater marker in various situations. Synthesis of the available research supports PMMoV as a useful enteric virus process indicator since its high concentrations in source water allow for identifying the extent of virus log-reductions in field, pilot, and full-scale (waste)water treatment systems. PMMoV reduction levels during many forms of wastewater treatment were less than or equal to the reduction of other viruses, suggesting this virus can serve as an enteric virus surrogate when evaluating new treatment technologies. PMMoV excels as an index virus for enteric viruses in environmental waters exposed to untreated domestic wastewater because it was detected more frequently and in higher concentrations than other human viruses in groundwater (72.2%) and surface waters (freshwater, 94.5% and coastal, 72.2%), with pathogen co-detection rates as high as 72.3%. Additionally, PMMoV is an important microbial source tracking marker, most appropriately associated with untreated domestic wastewater, where its pooled-specificity is 90% and pooled-sensitivity is 100%, as opposed to human feces where its pooled-sensitivity is only 11.3%. A limited number of studies have also suggested that PMMoV may be a useful index virus for enteric viruses in monitoring the microbial quality of fresh produce and shellfish, but further research is needed on these topics. Finally, future work is needed to fill in knowledge gaps regarding PMMoV's global specificity and sensitivity.

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Section: Pepper Mild Mottle Virus Ecology and Its Origin In Human Fecesmentioning

confidence: 99%

Pepper mild mottle virus: A plant pathogen with a greater purpose in (waste)water treatment development and public health management

et al. 2018

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“…Given that any of the evolutionary prediction models we are building is as good as the starting datasets and underlying bioinformatics algorithms are, securing a critical amount of relevant data is essential for any credible prediction. Besides mutations leading to amino acid replacements, synonymous nucleotide changes may also contribute to different viral pathogenicity levels, as was already shown for another positive-sense single-stranded RNA virus [30]. Therefore, all detected nucleotide changes, even the silent ones, should be taken into account when conducting data mining analysis and viral genotype−phenotype association SARS-CoV-2 studies.…”

Section: Discussionmentioning

confidence: 97%

First whole-genome analysis of the novel coronavirus (SARS-CoV-2) obtained from COVID-19 patients from five districts in Western Serbia

Vidanović¹,

Tešović²,

Volkening

et al. 2021

Epidemiol. Infect.

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This study was endeavoured to contribute in furthering our understanding of the molecular epidemiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by sequencing and analysing the first full-length genome sequences obtained from 48 coronavirus disease-2019 (COVID-19) patients in five districts in Western Serbia in the period April 2020–July 2020. SARS-CoV-2 sequences in Western Serbia distinguished from the Wuhan sequence in 128 SNPs in total. The phylogenetic structure of local SARS-CoV-2 isolates suggested the existence of at least four distinct groups of SARS-CoV-2 strains in Western Serbia. The first group is the most similar to the strain from Italy. These isolates included two 20A sequences and 15−30 20B sequences that displayed a newly occurring set of four conjoined mutations. The second group is the most similar to the strain from France, carrying two mutations and belonged to 20A clade. The third group is the most similar to the strain from Switzerland carrying four co-occurring mutations and belonging to 20B clade. The fourth group is the most similar to another strain from France, displaying one mutation that gave rise to a single local isolate that belonged to 20A clade.

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“…A single amino acid mutation of asparagine to methionine at the 138th position (N138M) of the PMMoV-I isolate was sufficient to induce a hypersensitive response (HR) and localization of the virus in C. chinense plants with the L 3 gene (106). This mutation (N138M) is observed in all PMMoV isolates characterized as P 123 pathotypes (18,78,106,111). The mutations in PMMoV CP at the 7th position from alanine to serine (A7S), and the 81st position from serine to alanine (S81A) had L 3 -mediated resistance-inducing and -breaking abilities, respectively (112).…”

Section: Pathotypes Of Pmmov and The Role Of Viral Coat Protein In Th...mentioning

confidence: 98%

“…For instance, EcoRI restriction digestion of 836 bp amplicons of PMMoV-S genome (P 12 ) and PMMoV-Ia (P 123 ) genome obtained using primer pair P12/3 and P12/3A revealed two fragments of 260 and 570 bp, respectively, from the genome of PMMoV-Ia, whereas only a single fragment was obtained for PMMoV-S (65). The available genomic data of PMMoV were mined for identifying the informative sites in PMMoV genome for its pathotype determination (18). The findings indicate that the nucleotide composition at positions 552, 565, 639, 666, 708, 5921, 5975, and 6002 can serve as a reliable marker for distinguishing three PMMoV pathotypes, viz., P 12 , P 123 , and P 1234 (18).…”

Section: Pathotypes Of Pmmov and The Role Of Viral Coat Protein In Th...mentioning

confidence: 99%

“…Farmers and researchers face a significant challenge in controlling the spread of PMMoV due to the virus's ability to form highly stable viral particles. These particles can persist and remain infectious in a variety of environments, including irrigation and natural water sources, soil, compost, and plant debris (16)(17)(18). This makes it difficult to eliminate the virus and prevent its transmission among crops.…”

Section: Introductionmentioning

confidence: 99%

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Pepper mild mottle virus: a formidable foe of capsicum production—a review

Kumari,

Sharma,

Patel

et al. 2023

Front. Virol.

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Viruses are one of the major restraining factors in pepper cultivation globally. Among different viruses, pepper mild mottle virus (PMMoV) is one of the most detrimental plant viruses infecting Capsicum spp. belonging to the genus Tobamovirus and Virgaviridae family. It has a monopartite positive-sense single-stranded RNA genome of 6.35 kb size. On an average, PMMoV results in 15%–40% losses in capsicum fruit yield. However, the incidence of PMMoV can reach as high as 95%, leading to substantial yield losses ranging from 75% to 95%. The virus is transmitted via contact, soil, and seeds rather than via insect vectors. PMMoV, because of its seed-borne nature, now occurs worldwide. PMMoV mainly infects Capsicum spp. under natural conditions; however, it can experimentally be transmitted to other plants species belonging to the families Solanaceae, Cucurbitaceae, Labiatae, Chenopodiaceae, and Plantaginaceae. The resistance to tobamoviruses in capsicum is conferred by L locus. Mutations in the coat protein of PMMoV are responsible for the emergence of L-mediated resistance-breaking pathotypes. The highly contagious nature of the virus, seed transmission behavior, and the emergence of virulence complicate its management through a single approach. Therefore, efforts are directed towards providing a more practical and efficient integrated management solution using the RNA interference approach; exploitation of the L gene for resistance breeding; and the inhibitory potential of natural products, systemic resistance-inducing antagonistic bacteria, and chemically synthesized silver nanoparticles. Markers linked to L alleles have been observed to accelerate capsicum breeding programs through marker-assisted selection. In this study, an attempt has been made to compile the recent developments in PMMoV biology, pathogenic variability, genomic organization, and management strategies.

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Revealing new information from existing genomic data for pepper mild mottle virus pathotype determination

Cited by 4 publications

References 38 publications

Pepper mild mottle virus: A plant pathogen with a greater purpose in (waste)water treatment development and public health management

Pepper mild mottle virus: A plant pathogen with a greater purpose in (waste)water treatment development and public health management

First whole-genome analysis of the novel coronavirus (SARS-CoV-2) obtained from COVID-19 patients from five districts in Western Serbia

Pepper mild mottle virus: a formidable foe of capsicum production—a review

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