Characterization of the Complete Genome and P0 Protein for a Previously Unreported Genotype of Cotton Leafroll Dwarf Virus, an Introduced Polerovirus in the United States

Abstract

Virus-like disease symptoms consisting of leaf cupping, shortened internodes, and overall stunting were observed in commercial cotton fields in Alabama in 2017 to 2018. To determine the complete genome sequence of the suspected causal polerovirus, symptomatic leaf samples were collected in Macon County, Alabama, and subjected to Illumina RNA sequencing. Based on BLASTn analysis, the Illumina contig of 5,771 nt shared the highest nucleotide identity (approximately 95%) with members of the species Cotton leafroll dwarf virus (CLRDV) (genus Polerovirus; family Luteoviridae) from Argentina and Brazil. The full-length viral genome sequence was verified by reverse transcription (RT)-PCR amplification, cloning, and Sanger sequencing. The complete CLRDV genome of 5,865 nt in length shared 94.8 to 95.2% nucleotide identity with six previously reported CLRDV isolates. The genome of the CLRDV isolate amplified from Alabama samples (CLRDV-AL) has seven predicted open reading frames (ORFs). Viral proteins 1 to 5 (P1 to P5) shared 91.9 to 99.5% amino acid identity with the six CLRDV isolates from Argentina and Brazil. However, P0, the suppressor of host gene silencing, shared 82.4 to 88.5% pairwise amino acid identity with the latter CLRDV isolates. Phylogenetic analysis of the seven full-length CLRDV genomes resolved three sister clades: CLRDV-AL, CLRDV-typical, and CLRDV-atypical, respectively. Three recombination events were detected by the recombination detection program among the seven CLRDV isolates with breakpoints occurring along the genome. Pairwise nucleotide identity comparisons of ORF0 sequences for the three CLRDV-AL field isolates indicated that they were >99% identical, suggesting that this previously unknown CLRDV genotype represents a single introduction to Alabama.

Genome analysis of cotton leafroll dwarf virus reveals variability in the silencing suppressor protein, genotypes and genomic recombinants in the USA

“…CLRDV is considered an emerging disease in cotton in the USA. Although the viral genome of individual isolates each from Alabama [ 29 ], Georgia [ 30 ], and Texas [ 31 ] have been sequenced, no information is available on the genetic diversity and population structure of the virus. In this study, the nearly complete genome of six isolates from Georgia and one isolate from Alabama were sequenced, representing diverse symptoms, plant growth stage, and geographical locations to understand the genome variability of CLRDV in the USA.…”

Effect of Cotton Leafroll Dwarf Virus on Physiological Processes and Yield of Individual Cotton Plants

“…A few of the notable symptoms include reddening of leaves and petioles, leaf wilting, subsequent drooping, crinkling, and deformation of the leaves above the nodes, which had reddened leaves, development of intense green foliage, and shortening of upper internodes resulting in stunted plants (Tabassum et al, 2019(Tabassum et al, , 2020Bag et al, 2021). Severe disease infection could result in reduced boll set and lower seed-cotton yield per plant (Avelar et al, 2020). The disease symptomology can vary substantially depending upon plant developmental stage at the time of infection, stage of disease progression, location, and variety.…”

“…CLRDV is transmitted by the cotton aphid (Aphis gossypii L.; Avelar et al, 2020) in a circulative and persistent manner (Silva et al, 2008). CLRDV is a positive sense, single-stranded RNA virus, and it is a phloem-limited virus, meaning it replicates and circulates mainly in the phloem tissue of the host plant (Silva et al, 2008;Jiménez et al, 2021).…”

“…CLRDV is a positive sense, single-stranded RNA virus, and it is a phloem-limited virus, meaning it replicates and circulates mainly in the phloem tissue of the host plant (Silva et al, 2008;Jiménez et al, 2021). In the United States, the partial genome sequence of CLRDV was first sequenced from isolates collected from Alabama (Avelar et al, 2020), and the complete genome was subsequently completed from an isolate collected in Georgia (Tabassum et al, 2020(Tabassum et al, , 2021. The genomic sequence of the CLRDV isolate from Georgia was between 95 and 98% identical to the genome of other CLRDV isolates reported in the United States (Alabama, GenBank accession number MN071395; Texas, MN872302) and South America (KF359947, KF906261, KF906260, NC_014545, GU167940, and HQ827780; Tabassum et al, 2020Tabassum et al, , 2021.…”

Key Amino Acids for Pepper Vein Yellows Virus P0 Protein Pathogenicity, Gene Silencing, and Subcellular Localization

“…The ORF4 region, which is present within the CP gene, although on an alternative reading frame, leads to the expression of the viral movement protein. ORF5 can be expressed through casual CP termination codon suppression and also encodes the read-through domain, which is necessary for effective aphid transmission ( Ali et al, 2018 ; Agrofoglio et al, 2019 ; Avelar et al, 2020 ).…”