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

Abstract

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.

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

“…In addition, one mastrevirus, Chickpea chlorotic dwarf virus (CpCDV) has been reported in association with leaf curl symptoms in cotton in Pakistan [28]. The Cotton leaf curl Multan betasatellite (CLCuMB) is the only betasatellite species detected in association with the CLCuD complex in the Indian subcontinent [7,[21][22]25,29,30]. A number of different alphasatellites, Cotton leaf curl Multan alphasatellite (CLCuMuA), Cotton leaf curl Lucknow alphasatellite (CLCuLuA), Gossypium darwinii symptomless alphasatellite (GDarSLA) and Gossypium mustilinum symptomless alphasatellite (GMusSLA) have been reported to be associated with the CLCuD complex in this subcontinent [7,[21][22]25,29,31].…”

“…The Cotton leaf curl Multan betasatellite (CLCuMB) is the only betasatellite species detected in association with the CLCuD complex in the Indian subcontinent [7,[21][22]25,29,30]. A number of different alphasatellites, Cotton leaf curl Multan alphasatellite (CLCuMuA), Cotton leaf curl Lucknow alphasatellite (CLCuLuA), Gossypium darwinii symptomless alphasatellite (GDarSLA) and Gossypium mustilinum symptomless alphasatellite (GMusSLA) have been reported to be associated with the CLCuD complex in this subcontinent [7,[21][22]25,29,31]. The recombination phenomenon is a major driving force in the evolution of begomovirus genomes [32][33][34][35] including CLCuD-begomoviruses [7,25,36].…”

Agroterrorism in Indian Context

“…Apart from badly shattering the national economy; unable to withstand losses, at least 15 cotton farmers committed suicide, triggering violent protests and socio-political chaos in punjab [51][52] . A thorough investigation of outbreak associated virus complex (virus and associated alpha and beta satellite molecules) sequences revealed clear evidence of phylogenetic and epidemiological relatedness with recently evolved virus complexes reported from pakistan [53][54][55] . These sequences (from India and pakistan) denoted a novel clade of CLCuMuV, distinct from previously circulating strains, and had unique recombination patterns 53,54 .…”

“…Unusually however, virus sequences associated with 2015 CLCuD outbreak have not been reported from any of the farmer's fields in pakistan till date. Rather, these virus complex sequences were actually detected and reported only from experimental cotton plants (cultivated and non-cultivated varieties), maintained at two different cotton research institutes (Cotton Research Station, Vehari and Central Cotton Research Institute, Multan) situated in the punjab province of pakistan [53][54][55] . In fact, these research stations have maintained infective virus complexes from the first CLCuD epidemic (occurred during 1990s), from which the recent virus complex is suggested to have evolved through recombination 49,[53][54][55] .…”

“…Rather, these virus complex sequences were actually detected and reported only from experimental cotton plants (cultivated and non-cultivated varieties), maintained at two different cotton research institutes (Cotton Research Station, Vehari and Central Cotton Research Institute, Multan) situated in the punjab province of pakistan [53][54][55] . In fact, these research stations have maintained infective virus complexes from the first CLCuD epidemic (occurred during 1990s), from which the recent virus complex is suggested to have evolved through recombination 49,[53][54][55] . Taken together, finding of newly evolved CLCuMuV sequences exclusively from experimental plants in research stations in pakistan, followed by trans-border outbreak of the virus complexes in India without the involvement of farmer's fields in pakistan side, do not appear to signify a natural pattern of transmission.…”