Cotton Leafroll Dwarf Virus US Genomes Comprise Divergent Subpopulations and Harbor Extensive Variability

Abstract

Cotton leafroll dwarf virus (CLRDV) was first reported in the United States (US) in 2017 from cotton plants in Alabama (AL) and has become widespread in cotton-growing states of the southern US. To investigate the genomic variability among CLRDV isolates in the US, complete genomes of the virus were obtained from infected cotton plants displaying mild to severe symptoms from AL, Florida, and Texas. Eight CLRDV genomes were determined, ranging in size from 5865 to 5867 bp, and shared highest nucleotide identity with other CLRDV isolates in the US, at 95.9–98.7%. Open reading frame (ORF) 0, encoding the P0 silencing suppressor, was the most variable gene, sharing 88.5–99.6% and 81.2–89.3% amino acid similarity with CLRDV isolates reported in cotton growing states in the US and in Argentina and Brazil in South America, respectively. Based on Bayesian analysis, the complete CLRDV genomes from cotton in the US formed a monophyletic group comprising three relatively divergent sister clades, whereas CLRDV genotypes from South America clustered as closely related sister-groups, separate from US isolates, patterns reminiscent of phylogeographical structuring. The CLRDV isolates exhibited a complex pattern of recombination, with most breakpoints evident in ORFs 2 and 3, and ORF5. Despite extensive nucleotide diversity among all available CLRDV genomes, purifying selection (dN/dS < 1) was implicated as the primary selective force acting on viral protein evolution.

Complete Genome Sequence of Cotton Leafroll Dwarf Virus Infecting Cotton in Oklahoma, USA

“…Using areas of overlap between the sequences, the Illumina and Sanger sequencing results were combined, resulting in a complete genome of CLRDV isolate EC4, which was 5,866 nucleotides in length. BLASTn (NCBI) searches of the GenBank nonredundant database showed that CLRDV isolate EC4 shared 99.22% nucleotide identity and 98.03% amino acid identity with CLRDV isolate CT2 (GenBank accession number OK185941.1 ) from Texas ( 13 ), which is supported by the MEGA X phylogenetic analysis ( Fig. 1 ).…”

“…Thereafter, it was reported in cotton fields in almost a dozen states ( 2 – 12 ). CLRDV has a positive single-stranded RNA genome of approximately 5,865 nucleotides ( 13 ).…”

Cotton leafroll dwarf disease: An enigmatic viral disease in cotton

“…These data might be helpful in further understanding the diversity, degree of genetic differentiation, and population dynamics of CLRDV. A recent study suggests that eight newly determined full‐length genome sequences of CLRDV isolated from cotton plants in Alabama, Florida, and Texas were phylogenetically related with a CLRDV genotype from Alabama (Ramos‐Sobrinho et al, 2021). Furthermore, these isolates have been shown to cluster into a monophyletic group among the CLRDV populations in North America.…”

The Viral Threat in Cotton: How New and Emerging Technologies Accelerate Virus Identification and Virus Resistance Breeding

“…The cotton leaf roll dwarf virus (CLRDV, Genus: Polerovirus ; Family: Solemoviridae ), a positive sense (+) ssRNA virus, causes the Cotton Blue Disease (CBD) that affects cotton crops in South America and Africa ( Distéfano et al, 2010 ; Parkash et al, 2021 ). Aphis gossypii (Glover; Hemiptera: Aphididae ), one of the most polyphagous aphid species and worldwide-distributed, hosts over 40 viruses ( Quan et al, 2019 ) and is the exclusive vector of CLRDV ( Michelotto and Busoli, 2007 ; Ramos-sobrinho et al, 2021 ).…”

“…Since 2017, CBD has spread in important cotton grower states in the United States ( Avelar et al, 2019 ; Parkash et al, 2021 ; Ramos-sobrinho et al, 2021 ). Curiously, due to very rigorous winters, A. gossypii does not impose high pressure in the United States cotton fields ( Carletto et al, 2009 ), suggesting two hypotheses: first, CLRDV may have adapted to a new viral vector and second, even in low aphid pressure, the insects can perpetuate disease spread and maintenance.…”