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Ecology and Epidemiology of Wheat Curl Mite and Mite-Transmissible Viruses in Colorado and Insights into the Wheat Virome

10 Aug 2020-bioRxiv (Cold Spring Harbor Laboratory)-
TL;DR: Variation in WSMV resistance among wheat varieties; however a variety that harbored dual resistance to mite and W SMV had lower virus titer compared to varieties that contained single resistance gene, which suggests that pyramiding genes will ensure improved and durable resistance.
Abstract: The wheat curl mite (WCM)-transmissible wheat streak disease complex is the most serious disease of wheat in the U.S. Great Plains. In the current study, we determined the genetic variability in WCM and mite-transmitted viruses in Colorado and identified sources of resistance in Colorado wheat germplasm to wheat streak disease complex. We identified two distinct genotypes of WCM, Type 1 and Type 2 based on the ribosomal ITS1 region. Both genotypes were found to co-exist throughout the wheat producing regions of Colorado. Analysis of the whole genome and partial coat protein sequences revealed rich diversity of wheat streak mosaic virus (WSMV) and High Plains wheat mosaic virus (HPWMoV) isolates collected from Colorado, whereas triticum mosaic virus (TriMV) showed low sequence variability. Analysis of WSMV isolates revealed two novel isolates and one that was 100% similar to a new variant of WSMV from Kansas. Interestingly, between 2-4 genotypes of all 8 RNA segments of HPWMoV were identified, which suggests new variants of emaraviruses and co-occurrence of multiple strains within host populations. Several novel viruses including mycoviruses were identified for the first time in Colorado. We found variation in WSMV resistance among wheat varieties; however a variety that harbored dual resistance to mite and WSMV had lower virus titer compared to varieties that contained single resistance gene. This suggests that pyramiding genes will ensure improved and durable resistance. Future research may be aimed at elucidating the dynamics, diversity, and distribution of the new WSMV and HPWMoV isolates and their responses to wheat genotypes.

Summary (2 min read)

Wheat Curl Mite and Plant Tissue Collection

  • Plants were examined using a dissecting microscope for the presence of WCMs.
  • Plants were grown in gallon pots with 2-3 plants per pot in Promix HP © soil.
  • Additionally, leaf tissues were tested for presence of WSMV, TriMV and HPWMoV.

Virus Detection and Quantification

  • Total RNA was extracted from approximately 40 mg homogenized leaf tissues obtained from various sources described above, lysed in Trisure® (Bioline Meridian Bioscience) using Direct-zol® RNA Purification Kit (Zymo Research, CA, USA) according to the manufacturer's recommendations.
  • The quantity of RNA was approximated using a NanoDrop One spectrophotometer (Thermo Fisher Scientific, MA, USA) and stored at -80°C until virus quantification.
  • To detect and quantify WSMV and TriMV, approximately 50 ng of RNA was used in a previously published qRT-PCR duplex assay (Price et al. 2010) with the TaqMan® RNA-to-Ct™ 1-step kit (Applied Biosystems™, ThermoFisher Scientific) on a QuantStudio™3 Real-Time PCR system (Applied Biosystems™, ThermoFisher Scientific).
  • Field samples with CQ values above the lower detection limit, as defined by the standard curves described below, were considered to be positive for the specified virus.
  • To detect HPWMoV, complementary DNA (cDNA) was synthesized from 1 μg of total RNA using the Verso® cDNA Synthesis Kit (ThermoFisher Scientific).

Wheat Virome Analysis

  • Four leaf tissue samples that previously tested positive for WSMV from Larimer county., positive for WSMV and TriMV from Bent county., positive for WSMV and HPWMoV from Phillips county., and positive for WSMV and TriMV from Kit Carson county.
  • After all filtering operations, an average of 0.25x10 6 reads (3%) remained per dataset.
  • Then, analysis of SNPs for the viruses from assembled virome data were performed using the Tablet software program to determine genetic diversity.
  • Lastly, the raw sequence data was deposited in the NCBI Sequence Read Archive (SRA) repository under submission number SUB7870854.
  • Phylogenetic analysis of the complete sequences of the nucleoprotein encoding RNA3 segments of members of both groups of HPWMoV and three variants all from the Phillips county sample, shows version Colorado RNA3C (MT762120) is similar to isolates from OH/TX or group A (Fig. 5 ).

Wheat Germplasm and Virulence Test

  • A natural infection of wheat streak mosaic virus was observed in the Colorado State University Irrigated Variety Performance Trial (IVPT) at Burlington, CO, in 2019.
  • The trial included 24 different genotypes (released varieties and experimental lines), planted in a randomized complete block design with three replications.
  • To quantify virus titer in wheat varieties, 10 leaf samples were collected on June 21, 2019.
  • All ten leaves were stacked, and a small section of tissue was cut from the center of the stack.

Virus Occurence in Colorado

  • Survey of WCM-transmitted viruses revealed the presence of all three economicallyimportant viruses in Colorado, WSMV, TriMV and HPWMoV (Fig. 2 ).
  • Of the 40 symptomatic samples tested, 38 were positive for one or more WCM-transmitted viruses.
  • WSMV was found in all surveyed counties (Fig. 2.

Identification of Virus Genotypes

  • To determine the genetic variability among WSMV isolates in Colorado, the authors sequenced a portion of the WSMV-NIb region and performed phylogenetic analyses with isolates from other wheat producing states in the U.S. and other regions of the world.
  • Interestingly, an isolate, Larimer county 1, was 100% similar to a Kansas isolate (MK318278) that was collected from a wheat variety carrying the Wsm2 virus resistance gene that is known to confer resistance to WSMV (Fellers et al. 2019) .
  • The isolate Larimer county 2 collected from same location as the Larimer county 1 isolate, appeared to be genetically distinct from other isolates in the U.S.
  • In contrast, to the genetic diversity in WSMV isolates, there was limited variability in TriMV isolates collected in Colorado compared to that of other sequenced isolates.
  • Phylogenetic analysis reveals two distinct groups of the HPWMoV isolates among available HPWMoV nucleoprotein sequences as observed by previous studies (Stewart 2016) .

Virus Resistance in Variety Trial

  • Wheat varieity trial included a combination of 24 public and private varieties and experimental lines.
  • Seed companies with entries in the variety trials included AgriMaxx Wheat, AgriPro Syngenta, Dyna-Gro Seed, Limagrain Cereal Seeds, and WestBred Bayer.
  • The gerplasm included varieties with no known resistance, a single resistance marker to either WCM (WCM6D) or WSMV (Wsm2), and one variety, Guardian, with both resistance markers, WCM6D and Wsm2 (Table 4 ).

Discussion

  • Mite-vectored wheat viruses continue to cause significant yield losses in Colorado.
  • Wheat virome analysis confirmed the presence of known viruses such as WSMV, TriMV and HPWMoV, but also revealed presence of several mycoviruses and a novel Ixeridium yellow mottle virus 2 from Colorado wheat samples.
  • The genetic diversity of WSMV has been evaluated among various isolates in the U.S. and from around the world by sequencing the coat protein (CP) (Robinson and Murray 2013) and more recent whole genome sequencing (Schubert et al. 2015) .
  • There have been reports of increasing mite populations and virus infection in resistant varieties (Tatineni and Hein 2018) .

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Figures (10)

Content maybe subject to copyright    Report

1
Ecology and Epidemiology of Wheat Curl Mite and Mite-Transmissible Viruses in 1
Colorado and Insights into the Wheat Virome 2
3
Tessa Albrecht
1
, Samantha White
1
, Marylee Layton
2
, Mark Stenglein
2
, Scott Haley
3
4
and Punya Nachappa
1
5
1
Department of Agricultural Biology, Colorado State University, 307 University Ave, Fort 6
Collins, CO 80523 7
2
Department of Microbiology, Immunology, and Pathology, College of Veterinary 8
Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, 9
U.S.A. 10
3
Department of Soil and Crop Sciences, Colorado State University, 307 University Ave, 11
Fort Collins, CO 80523 12
13
Corresponding author: Punya Nachappa; E-mail: punya.nachappa@colostate.edu 14
Keywords: wheat curl mite, wheat streak mosaic virus, triticum mosaic virus, High 15
Plains wheat mosaic virus, resistance, virome 16
Funding: Colorado Wheat Research Foundation, Colorado Wheat Administrative 17
Committee 18
19
.CC-BY-ND 4.0 International licenseavailable under a
(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
The copyright holder for this preprintthis version posted August 10, 2020. ; https://doi.org/10.1101/2020.08.10.244806doi: bioRxiv preprint

2
Abstract 20
The wheat curl mite (WCM)-transmissible wheat streak disease complex is the most serious 21
disease of wheat in the U.S. Great Plains. In the current study, we determined the genetic 22
variability in WCM and mite-transmitted viruses in Colorado and identified sources of resistance 23
in Colorado wheat germplasm to wheat streak disease complex. We identified two distinct 24
genotypes of WCM, Type 1 and Type 2 based on the ribosomal ITS1 region. Both genotypes 25
were found to co-exist throughout the wheat producing regions of Colorado. Analysis of the 26
whole genome and partial coat protein sequences revealed rich diversity of wheat streak mosaic 27
virus (WSMV) and High Plains wheat mosaic virus (HPWMoV) isolates collected from 28
Colorado, whereas triticum mosaic virus (TriMV) showed low sequence variability. Analysis of 29
WSMV isolates revealed two novel isolates and one that was 100% similar to a new variant of 30
WSMV from Kansas. Interestingly, between 2-4 genotypes of all 8 RNA segments of HPWMoV 31
were identified, which suggests new variants of emaraviruses and co-occurrence of multiple 32
strains within host populations. Several novel viruses including mycoviruses were identified for 33
the first time in Colorado. We found variation in WSMV resistance among wheat varieties; 34
however a variety that harbored dual resistance to mite and WSMV had lower virus titer 35
compared to varieties that contained single resistance gene. This suggests that pyramiding genes 36
will ensure improved and durable resistance. Future research may be aimed at elucidating the 37
dynamics, diversity, and distribution of the new WSMV and HPWMoV isolates and their 38
responses to wheat genotypes. 39
40
Keywords: wheat curl mite, wheat streak mosaic virus, triticum mosaic virus, high plains wheat 41
mosaic virus, resistance, virome42
.CC-BY-ND 4.0 International licenseavailable under a
(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
The copyright holder for this preprintthis version posted August 10, 2020. ; https://doi.org/10.1101/2020.08.10.244806doi: bioRxiv preprint

3
Wheat (Triticum aestivum L.) is considered the most important crop in the 21
st
century as it 43
serves as a nutritional source of calories and protein in the human diet worldwide (Arzani and 44
Ashraf 2017; Curtis and Halford 2014). In the United States, wheat ranks third among field 45
crops in planted acreage, production, and gross farm receipts, behind corn and soybeans (USDA-46
ERS 2019). Among the top 10 wheat growing states, Colorado ranked 6
th
in 2019 with 2,150,000 47
acres being planted and a yield of 49 bushels per acre resulting in total production of 98,000,000 48
bushels valued at $387,100,000 (USDA-NASS 2019). The wheat curl mite (WCM), Aceria 49
tosichella Keifer (Acari: Eriophyidae) is a globally important pest affecting wheat production in 50
the Americas, Europe, and Asia (Skoracka et al. 2018). The mite causes direct damage by 51
feeding, which can reduce cereal yield (Harvey et al. 2000). But more importantly, WCM-52
transmitted viruses including wheat streak mosaic virus (family Potyviridae/genus Tritimovirus; 53
acronym WSMV) (Slykhuis 1955), triticum mosaic virus (Potyviridae/Poacevirus; TriMV) 54
(Seifers et al. 2009) and High plains wheat mosaic virus (Fimoviridae/Emaravirus; HPWMoV) 55
(Seifers et al. 1997) are among the most significant viruses in U.S. agriculture, responsible for 56
yield losses in wheat, barley, oats and rye (Burrows et al. 2009; Navia et al. 2013). Average 57
yield losses from the WCM-WSMV complex range from 5 to 7% in the US Great Plains, but 58
100% yield losses may occur in some fields (Appel et al. 2015). 59
Worldwide, the WCM has been found to be a diverse species complex with numerous 60
genetic lineages (Skoracka et al. 2018). In North America however, only two genetically distinct 61
genotypes of WCM have been characterized based on ribosomal ITS1 and mitochondrial 62
Cytochrome oxidase I/II partial sequences: Type 1, initially identified from South Dakota, 63
Kansas, Montana, Nebraska and Texas, and Type 2, from Nebraska (Hein et al. 2012). Both 64
genotypes occur in mixed populations in wheat-producing areas of the U.S. Great Plains. The 65
.CC-BY-ND 4.0 International licenseavailable under a
(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
The copyright holder for this preprintthis version posted August 10, 2020. ; https://doi.org/10.1101/2020.08.10.244806doi: bioRxiv preprint

4
two distinct genotypes demonstrate different responses to curl mite colonization (Cmc) genes; 66
Cmc1, Cmc2, Cmc3 and Cmc4 (Dhakal et al. 2017; Harvey et al. 1999) and differential viral 67
transmission efficiencies (Hein et al. 2012; McMechan et al. 2014; Seifers et al. 2002; Wosula 68
et al. 2016). For example, Type 2 is more virulent and makes wheat lines carrying the 1AL.1RS 69
(Cmc3 resistance gene) susceptible (Dhakal et al., 2017) and Type 2 mites transmit WSMV at 70
higher rates compared to Type 1 mites (Wosula et al., 2016). 71
The WSMV populations are complex as well with numerous genotypes (Robinson and 72
Murray 2013; Schubert et al. 2015), although different genotypes rarely occur in the same plant 73
(McNeil et al. 1996). In the U.S., there are two WSMV isolates, Sidney 81 and Type, sharing 74
97.6% nucleotide sequence identity, and produce similar symptoms in wheat (Choi et al. 2001; 75
Hall et al. 2001). A third isolate, El Batán, from Mexico has diverged from the American strains 76
and has 79% nucleotide sequence identity to Sidney 81 and Type (Choi et al. 2001). In contrast, 77
TriMV field populations showed minimal amounts of sequence variation suggesting that the 78
populations are very homogenous (Fuentes-Bueno et al. 2011). There is little information about 79
the phylogenetic relationships between HPWMoV isolates. There appears to be two distinct 80
groups of HPWMoV isolates within the U.S. (Stewart 2016). Currently there are three sources of 81
host resistance to WSMV - Wsm1, Wsm2, and Wsm3 (Liu et al. 2011; Lu et al. 2011; Triebe et 82
al. 1991). However, some of these resistance alleles are temperature sensitive and do not prevent 83
virus infection and replication above 18°C (Fahim et al. 2012). More recently, a novel QTL was 84
identified on wheat chromosome 6DS from the wheat cultivar, TAM112, which provides WCM 85
resistance and moderate WSMV resistance (Dhakal et al. 2018). Genes for resistance to TriMV 86
and HPWMoV have not been identified. 87
.CC-BY-ND 4.0 International licenseavailable under a
(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
The copyright holder for this preprintthis version posted August 10, 2020. ; https://doi.org/10.1101/2020.08.10.244806doi: bioRxiv preprint

5
One of the most effective ways of controlling WCM-virus complex is by planting mite 88
and disease resistant varieties; however, knowledge of mite and virus genotypes occurring in a 89
given area is critical because these genetic differences correspond to biological responses at the 90
phenotypic level (Hein et al. 2012). While Colorado is a major wheat producing state, there is no 91
information about the WCM-virus complex in the region. Moreover, little is known about 92
emerging and/or novel viruses of wheat in Colorado. Next generation sequencing is a powerful 93
tool that allows researchers to detect and characterize novel viruses (and bacterial and fungal 94
pathogens) and explore their diversity and pathogenicity in agricultural crops (Villamor et al. 95
2019). NGS is finding increased applications in revealing the viromes that contribute to the 96
disease phenotype. The term “virome” is defined as the genomes of all the viruses inhabiting a 97
specific organism or environment. In the current study, we determined the genetic variability in 98
WCM and mite-transmitted viruses in Colorado and identified sources of resistance in Colorado 99
wheat germplasm to WSMV and TriMV. In addition, we investigated the viromes of wheat from 100
four different locations in Colorado. To our knowledge, our study is among the first to report on 101
the wheat virome in the U.S. 102
103
Materials and Methods 104
Wheat Curl Mite and Plant Tissue Collection 105
Symptomatic wheat leaf tissues were collected across eastern Colorado by researchers, extension 106
agents and producers and delivered to our laboratory at Colorado State University. Plants were 107
examined using a dissecting microscope for the presence of WCMs. If present, mites were 108
transferred to healthy wheat plants of susceptible wheat varieties, Pronghorn or Hatcher at the 109
four-leaf stage or older. Plants were grown in gallon pots with 2-3 plants per pot in Promix HP
©
110
.CC-BY-ND 4.0 International licenseavailable under a
(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
The copyright holder for this preprintthis version posted August 10, 2020. ; https://doi.org/10.1101/2020.08.10.244806doi: bioRxiv preprint

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TL;DR: This report integrates the current state of knowledge of WCM–virus-plant interactions and addresses knowledge gaps regarding the mechanisms driving WCM infestation, viral epidemics, and plant responses.
Abstract: Wheat production and sustainability are steadily threatened by pests and pathogens in both wealthy and developing countries. This review is focused on the wheat curl mite (WCM), Aceria tosichella, and its relationship with wheat. WCM is a major pest of wheat and other cereals and a vector of at least four damaging plant viruses (Wheat streak mosaic virus, High plains wheat mosaic virus, Brome streak mosaic virus, and Triticum mosaic virus). The WCM–virus pathosystem causes considerable yield losses worldwide and its severity increases significantly when mixed-virus infections occur. Chemical control strategies are largely ineffective because WCM occupies secluded niches on the plant, e.g., leaf sheaths or curled leaves in the whorl. The challenge of effectively managing this pest–virus complex is exacerbated by the existence of divergent WCM lineages that differ in host-colonization and virus-transmission abilities. We highlight research progress in mite ecology and virus epidemiology that affect management and development of cereal cultivars with WCM- and virus-resistance genes. We also address the challenge of avoiding both agronomically deleterious side effects and selection for field populations of WCM that can overcome these resistance genes. This report integrates the current state of knowledge of WCM–virus-plant interactions and addresses knowledge gaps regarding the mechanisms driving WCM infestation, viral epidemics, and plant responses. We discuss the potential application of molecular methods (e.g., transcriptomics, epigenetics, and whole-genome sequencing) to understand the chemical and cellular interface between the wheat plant and WCM–virus complexes.

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References
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Journal ArticleDOI
TL;DR: Results of this study suggest that there are three main and many minor lineages of WSMV cocirculating in the region, and the W SMV population structure is consistent with a quasispecies model.
Abstract: A reverse transcriptase-polymerase chain reaction (RT-PCR) assay was developed to amplify cDNA from the coat protein coding region and 3'-noncoding region of the genome of wheat streak mosaic rymovirus (WSMV). AluI restriction fragment length polymorphisms (RFLPs) were found among RT-PCR products of four spatially or temporally distinct WSMV isolates. RT-PCR and RFLP analyses were then applied to examine intra- and interfield genetic variation in natural WSMV populations in 1994 and 1995. A total of 32 distinct RFLP types were found in five Nebraska counties, but most isolates could be grouped into three predominant genotypes. Chi-square analysis of the degree of sequence heterogeneity of isolates within fields, among fields in each county, and among counties indicated that there was as much variation within fields as among counties. There was, however, a significant difference (P = 0.001) in the frequencies of WSMV RFLP types between 1994 and 1995. Results of this study suggest that there are three main and many minor lineages of WSMV cocirculating in the region. The WSMV population structure is consistent with a quasispecies model. Isolates with distinctive RFLP patterns should facilitate future studies of WSMV dispersal.

74 citations

Journal ArticleDOI
TL;DR: In 2008, field surveys in 2008 determined the prevalence and diversity of viruses present in the Great Plains wheat crops as mentioned in this paper, and Symptomatic plants (n = 754) in nine states were tested for Wheat streak m...
Abstract: Field surveys in 2008 determined the prevalence and diversity of viruses present in the Great Plains wheat crops. Symptomatic plants (n = 754) in nine states were tested for Wheat streak m...

73 citations

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TL;DR: This work used metagenomic sequencing to survey the viral diversity present in captive arenavirus-infected snakes, and determined the complete or near complete sequence of 210 genome segments that grouped into 23 L and 11 S genotypes.
Abstract: Arenaviruses are one of the largest families of human hemorrhagic fever viruses and are known to infect both mammals and snakes. Arenaviruses package a large (L) and small (S) genome segment in their virions. For segmented RNA viruses like these, novel genotypes can be generated through mutation, recombination, and reassortment. Although it is believed that an ancient recombination event led to the emergence of a new lineage of mammalian arenaviruses, neither recombination nor reassortment has been definitively documented in natural arenavirus infections. Here, we used metagenomic sequencing to survey the viral diversity present in captive arenavirus-infected snakes. From 48 infected animals, we determined the complete or near complete sequence of 210 genome segments that grouped into 23 L and 11 S genotypes. The majority of snakes were multiply infected, with up to 4 distinct S and 11 distinct L segment genotypes in individual animals. This S/L imbalance was typical: in all cases intrahost L segment genotypes outnumbered S genotypes, and a particular S segment genotype dominated in individual animals and at a population level. We corroborated sequencing results by qRT-PCR and virus isolation, and isolates replicated as ensembles in culture. Numerous instances of recombination and reassortment were detected, including recombinant segments with unusual organizations featuring 2 intergenic regions and superfluous content, which were capable of stable replication and transmission despite their atypical structures. Overall, this represents intrahost diversity of an extent and form that goes well beyond what has been observed for arenaviruses or for viruses in general. This diversity can be plausibly attributed to the captive intermingling of sub-clinically infected wild-caught snakes. Thus, beyond providing a unique opportunity to study arenavirus evolution and adaptation, these findings allow the investigation of unintended anthropogenic impacts on viral ecology, diversity, and disease potential.

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"Ecology and Epidemiology of Wheat C..." refers background in this paper

  • ...Multiple infections involving variable numbers of genome segments has been described for snake-infecting reptarenavirues, which, like the emaraviruses, belong to the Bunyavirales order (Stenglein et al. 2015)....

    [...]

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TL;DR: WCMs collected at different times or locations may vary in their responses to different sources of resistance; therefore, testing mites for their response to resistance genes advanced in breeding programs may be needed before resistant cultivars are deployed in the field.
Abstract: Wheat (Triticum aestivum L.) yield is limited by wheat streak mosaic virus which is vectored by the wheat curl mite (WCM) Aceria tosicheilla (Keifer). Host resistance to WCM has reduced losses. This study was conducted to evaluate the effectiveness of resistance in wheat to WCM collected from various locations in the Great Plains. Collections of WCM from Montana, Nebraska, South Dakota, Texas, Alberta, Canada, and eight locations in Kansas were compared for their ability to survive and reproduce in the greenhouse on seven lines of wheat and wheat relatives previously identified as resistant. The lines and their sources of resistance were: AC PGR16635 (Aegilops tauschii Coss., Cmc1), PI525452 (Thinopyrum ponticum (Podp.) Liu and Wang, Cmc2), KS96WGRC40 (Ae. tauschii and Secale cereale L.), TA920 (Triticum timopheevii (Zhuk.) Zhuk spp. armenidcum), PI 475772 (S. cereale), TAM 107' (S. cereale), PI 222655 (T. aestivum). KS96WGRC40 and TA920 were the only entries that were resistant to all WCM collections. Other sources of resistance were effective against WCMs from some but not all locations. PI 222655 was resistant to WCMs from Nebraska and central Kansas but not to mites from most other locations. WCMs that were virulent to TAM 107 generally were also virulent to PIs 222655 and 475772 but avirulent to Cmc2. The WCMs from western Kansas, where TAM 107 is widely grown, were generally more virulent to that cultivar than WCM from central Kansas where the hectarage of TAM 107 is smaller. WCMs collected at different times or locations may vary in their responses to different sources of resistance; therefore, testing mites for their response to resistance genes advanced in breeding programs may be needed before resistant cultivars are deployed in the field.

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"Ecology and Epidemiology of Wheat C..." refers background in this paper

  • ...The variability in the WCM populations in a region can affect the prevalence and severity of virus infection (Wosula et al. 2016) and responses to WCM resistance genes (Dhakal et al. 2017; Harvey et al. 1999)....

    [...]