When human samples are sequenced, many assembled contigs are "unknown", as conventional alignments find no similarity to known sequences. Hidden Markov models (HMM) exploit the positions of specific nucleotides in protein-encoding codons in various microbes. The algorithm HMMER3 implements HMM using a reference set of sequences encoding viral proteins, "vFam". We used HMMER3 analysis of "unknow...

In the attempt to identify the causal agent of Citrus chlorotic dwarf disease (CCDD), a virus-like disorder of citrus, the small RNA fraction and total DNA from symptomatic citrus plants were subjected to high-throughput sequencing. DNA fragments deriving from an apparently new geminivirus-like agent were found and assembled by NGS to re-construct the entire viral genome. The newly identified v...

Watermelon chlorotic stunt virus (WmCSV) is a bipartite begomovirus (genus Begomovirus, family Geminiviridae) that causes economic losses to cucurbits, particularly watermelon, across the Middle East and North Africa. Recently squash (Cucurbita moschata) grown in an experimental field in Oman was found to display symptoms such as leaf curling, yellowing and stunting, typical of a begomovirus in...

The chickpea chlorotic dwarf virus (CpCDV) (from the genus Mastrevirus and family Geminiviridae) tomato leaf curl New Delhi (ToLCNDV) Begomovirus represent an important threat to different crops worldwide, as they are emerging viruses in Asian continent, were introduced Mediterranean region 2012, then reported Morocco 2017 2018. present study addresses dispersion of CpCDV ToLCNDV evaluates gene...

ABSTRACT The worldwide spread of Geminiviruses and its vector has been attributed to the high rate recombination, mutation, presence alternate hosts, transport plant material, global human activity along with trade, new agricultural practices climate change; therefore, most severe viral diseases among crops have grown in almost all regions world, including cassava Africa, cotton leaf curl disea...

Geminiviruses (Geminiviridae) are a diverse group of plant viruses differing from other known plant viruses in possessing circular, single-stranded DNA. Current classification divides the family into three subgroups, defined in part by genome organization, insect vector, and plant host range. Previous phylogenetic assessments of geminiviruses have used DNA and/or amino acid sequences from the r...

A previously undescribed monopartite begomovirus was identified in Kampot province, Cambodia, Malvastrum coromandelianum plants exhibiting yellow vein symptoms characteristic of infections. The apparently full-length viral component cloned and sequenced following enrichment circular DNA by rolling-circle amplification restriction enzyme digestion. genome the virus 2737 nucleotides length (KP188...