Molecular diagnostic development for begomovirus-betasatellite complexes undergoing diversification: A case study

Brown, Judith K.; Ur-Rehman, Muhammad Zia; Avelar, S.; Chingandu, Nomatter; Hameed, Usman; Haider, Saleem; Ilyas, Muhammad

doi:10.1016/j.virusres.2017.04.014

Cited by 18 publications

(16 citation statements)

References 39 publications

(50 reference statements)

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“…Our results indicate that although there is low intra-speci c diversity among our isolates, the haplotype number and haplotype diversity analyses revealed varying homogenous levels within the coding regions. Thus, the non-coding regions could have contributed to the overall low diversity indices, similar to the observations of [73].…”

Section: Discussionsupporting

confidence: 65%

Metagenomic analyses and genetic diversity of Tomato leaf curl virus complex affecting tomato plants in Kenya

Avedi

Adediji

Kilalo

et al. 2020

Preprint

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Background Tomato production is threatened worldwide by the occurrence of begomoviruses which are associated with tomato leaf curl diseases. There is little information on the molecular properties of tomato begomoviruses in Kenya, hence we investigated the population and genetic diversity of begomoviruses associated with tomato leaf curl in Kenya. Methods In 2018, we obtained tomato leaf samples with virus-like symptoms from farmers’ fields across Kenya and used Illumina sequencing to identify associated begomoviruses. Using the sequences, we determined the genetic diversity of begomoviruses. Additionally, selection pressure and recombinant isolates within the population were evaluated. Results Twelve complete begomovirus genomes were obtained from our samples with an average coverage of 99.9%. The sequences showed 95.7–99.7% identity among each other and 95.9–98.9% similarities with a Tomato leaf curl virus Arusha virus (ToLCArV) isolate from Tanzania. When we analyzed the amino acid sequences, we detected the highest identities in the regions coding for the coat protein gene (98.5–100%) within the isolates, and with the C4 gene of ToLCArV (97.1–100%). Phylogenetic algorithms clustered all Kenyan isolates in the same clades with ToLCArV, thus confirming the isolates to be a variant of the virus. Recombination analyses identified four putative events (P ≤ 0.05) among the isolates. Estimation of selection pressure within the virus population revealed the occurrence of negative or purifying selection in 5 out of the 6 coding regions. Conclusions The begomovirus associated with tomato leaf curl diseases in Kenya is a variant of ToLCArV possibly originating from Tanzania. Recombinant virus strains were detected within the population and there are divergence evolutionary events within the coding regions of the virus in Kenya. This information is useful in the development of appropriate management strategies for the disease.

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Section: Discussionsupporting

confidence: 65%

Metagenomic analyses and genetic diversity of Tomato leaf curl virus complex affecting tomato plants in Kenya

Avedi

Adediji

Kilalo

et al. 2020

Preprint

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“…The most widespread and core CLCuD-begomoviruses are Cotton leaf curl Alabad virus (CLCuAlV), Cotton leaf curl Kokhran virus (CLCuKoV), and Cotton leaf curl Multan virus (CLCuMuV) [7,21,22,24,25]. The non-core CLCuD-begomoviruses are Cotton leaf curl Bangalore virus (CLCuBaV), Cotton leaf curl Gezira virus (CLCuGeV), Okraenation leaf curl virus (OEnLCV), Papaya leaf curl virus (PaLCuV), Tomato leaf curl Bangalore virus (ToLCuBaV), Tomato leaf curl New Delhi virus (ToLCNDV), and occasionally associated with the CLCuD complex in the Indian subcontinent [21,24,26,27]. In addition, one mastrevirus, Chickpea chlorotic dwarf virus (CpCDV) has been reported in association with leaf curl symptoms in cotton in Pakistan [28].…”

Section: Introductionmentioning

confidence: 99%

Dominance of recombinant cotton leaf curl Multan-Rajasthan virus associated with cotton leaf curl disease outbreak in northwest India

et al. 2020

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Cotton leaf curl disease (CLCuD), caused by whitefly (Bemisiatabaci) transmitted singlestranded DNA viruses belonging to the Genus, Begomovirus (family, Geminiviridae) in association with satellite molecules; is responsible for major economic losses in cotton in three northwest (NW) Indian states Haryana, Punjab, and Rajasthan. Annual CLCuD incidences during 2012 to 2014 were estimated to be 37.5%, 63.6%, and 38.8% respectively. Cotton leaves were collected from symptomatic plants annually for three years and subjected to DNA isolation, followed by rolling circle amplification (RCA), cloning, and DNA sequencing of apparently full-length begomoviral genomes and associated betasatellites and alphasatellites. Among the thirteen CLCuD-begomoviral genomes recovered, eight were identified as Cotton leaf curl Multan virus-Rajasthan (CLCuMuV-Ra), one as-Pakistan (PK) and another as-Faisalabad (Fai), whereas, three were as Cotton leaf curl Kokhran virus-Burewala (CLCuKoV-Bu), indicating that CLCuMuV-Ra was the most prevalent begomovirus species. Five of the eight CLCuMuV-Ra sequences were found to be recombinants. The CLCuMuV-Ra-associated satellites consisted of Cotton leaf curl Multan betasatellite (CLCuMB), and Gossypium darwinii symptomless alphasatellite (GDarSLA), and Croton yellow vein mosaic alphasatellite (CrYVMoA). The second most abundant helper virus species, CLCuKoV-Bu, was associated with CLCuMB and GDarSLA.

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“…The genome of the CABs predominantly consists of a monopartite circular ssDNA (denoted as DNA-A) 3 , 5 , frequently associated with non-viral, single stranded circular satellite DNA molecules (alphasatellite and/or betasatellite), together presenting as an infection complex 3 , 6 , 7 . Though the role of alphasatellite is still enigmatic, betasatellite is instrumental in determining disease severity, symptoms and adaptability to the host 8 , 9 . Evolution of the CABs take place via frequent interspecific and/or intraspecific recombinations, which play an important role in emergence/re-emergence of recombinants having increased virulence, transmissibility and ability to overcome host resistance, eventually leading to epidemics 1 , 3 , 10 , 11 .…”

Section: Introductionmentioning

confidence: 99%

“…From the perspective of molecular epidemiology, distinct species of CLCuD complexes are endemic to the African and the Indian subcontinents 3 , 8 . Till date, African complex consisted of a single species of monopartite begomovirus, an alphasatellite and a betasatellite, the Cotton leaf curl Gezira virus (CLCuGeV), Cotton leaf curl Gezira alphasatellite (CLCuGeA) and the Cotton leaf curl Gezira betasatellite (CLCuGeB), respectively 3 , 12 .…”

Section: Introductionmentioning

confidence: 99%

“…The high genetic diversity of CABs corroborate with the diversity of other geminiviruses in this region, since the Indian subcontinent is considered as the centre for geminivirus origin, evolution and diversity 6 , 14 , 15 . In this region, at least four closely related CABs, namely the Cotton leaf curl Alabad virus (CLCuAlV), Cotton leaf curl Bangalore virus (CLCuBaV), Cotton leaf curl Kokhran virus (CLCuKoV) and the Cotton leaf curl Multan virus (CLCuMuV) have been identified as ‘core’ viruses, while CLCuGeV has been reported to be a recent introduction into this region 3 , 8 . Additionally, a number of other ‘non-core’ geminiviruses have also been reported to infect cotton in the Indian subcontinent, including Papaya leaf curl virus (PaLCuV), Chickpea chlorotic dwarf virus (CpCDV), Okra enation leaf curl virus (OEnLCV), Tomato leaf curl Bangalore virus (ToLCuBaV), and Tomato leaf curl New Delhi virus (ToLCNDV) 3 , 6 , 8 .…”

Section: Introductionmentioning

confidence: 99%

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Rebound of Cotton leaf curl Multan virus and its exclusive detection in cotton leaf curl disease outbreak, Punjab (India), 2015

Datta

Budhauliya

Das

et al. 2017

Sci Rep

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Cotton leaf curl disease (CLCuD) outbreaks caused by CLCuD associated begomoviruses (CABs) significantly constrain cotton production in India and Pakistan. In comparison to the CABs circulating in Pakistan, molecular epidemiology, evolution and recombination patterns of CABs circulating in India are less studied. In this work, we characterized CAB complex sequences obtained from the most recent outbreak (Punjab, India, 2015), and rigorously analyzed them with reference to GenBank sequences, submitted from India, Pakistan and other neighbouring countries, using contemporary bioinformatics approaches. In this manuscript, we illustrate the detection of a recombinant, phylogenetically distinct clade of Cotton leaf curl Multan virus (CLCuMuV), suggesting rebound of CLCuMuV in this region. Interestingly, we could not detect Cotton leaf curl Kokhran virus-Burewala strain (CLCuKoV-Bu), which was prevalent in this region, until now. Our study thus indicates substitution of the ‘virulent resistance breaking’ CLCuKoV-Bu by the re-emerging CLCuMuV recombinants. Our findings corroborate with that of a very recent study from Pakistan and we here discuss epidemiological links between the CAB complexes reported in these two studies. Taken together, these observations signify a shifting epidemiology of CABs, and seem to correlate with the recent prediction of the ‘third epidemic’ of CLCuD in the Indian subcontinent.

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Molecular diagnostic development for begomovirus-betasatellite complexes undergoing diversification: A case study

Cited by 18 publications

References 39 publications

Metagenomic analyses and genetic diversity of Tomato leaf curl virus complex affecting tomato plants in Kenya

Metagenomic analyses and genetic diversity of Tomato leaf curl virus complex affecting tomato plants in Kenya

Dominance of recombinant cotton leaf curl Multan-Rajasthan virus associated with cotton leaf curl disease outbreak in northwest India

Rebound of Cotton leaf curl Multan virus and its exclusive detection in cotton leaf curl disease outbreak, Punjab (India), 2015

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