RNA viral metagenome of whiteflies leads to the discovery and characterization of a whitefly-transmitted carlavirus in North America

Abstract

Whiteflies from the Bemisia tabaci species complex have the ability to transmit a large number of plant viruses and are some of the most detrimental pests in agriculture. Although whiteflies are known to transmit both DNA and RNA viruses, most of the diversity has been recorded for the former, specifically for the Begomovirus genus. This study investigated the total diversity of DNA and RNA viruses found in whiteflies collected from a single site in Florida to evaluate if there are additional, previously undetected viral types within the B. tabaci vector. Metagenomic analysis of viral DNA extracted from the whiteflies only resulted in the detection of begomoviruses. In contrast, whiteflies contained sequences similar to RNA viruses from divergent groups, with a diversity that extends beyond currently described viruses. The metagenomic analysis of whiteflies also led to the first report of a whitefly-transmitted RNA virus similar to Cowpea mild mottle virus (CpMMV Florida) (genus Carlavirus) in North America. Further investigation resulted in the detection of CpMMV Florida in native and cultivated plants growing near the original field site of whitefly collection and determination of its experimental host range. Analysis of complete CpMMV Florida genomes recovered from whiteflies and plants suggests that the current classification criteria for carlaviruses need to be reevaluated. Overall, metagenomic analysis supports that DNA plant viruses carried by B. tabaci are dominated by begomoviruses, whereas significantly less is known about RNA viruses present in this damaging insect vector.

Figure 1. Schematic genome organization of Cowpea mild mottle virus (CpMMV) isolates identified in Ghana (top) and Florida (middle) as well as the general genome organization observed in carlavirus species (bottom; exact species shown in phylogenetic tree in Figure 2).

Each block represents identified open reading frames (ORFs) in these genomes and the encoded protein names are given on top of the CpMMV Florida panel, including the replication polyprotein, triple gene block (TGB), capsid (CP), and nucleic acid binding (NB) protein. The four different domains within the replication polyprotein exhibiting viral methyltransferase, peptidase, superfamily one (SF1) helicase, and RNA-dependent RNA polymerase (polymerase) motifs are indicated. Percentage values in the CpMMV Ghana genome schematic represent amino acid pairwise identities among individual ORFs of CpMMV Ghana and CpMMV Florida. Percentages in the Carlaviruses genome schematic represent amino acid pairwise identity ranges observed between different carlavirus species and CpMMV Florida. ORFs highlighted in grey represent ORFs without a standard start codon (a lighter grey in the carlaviruses panel indicates that some carlavirus species have a standard start codon while others do not).

Figure 2. Maximum likelihood phylogenetic tree of capsid proteins (CP) found in different carlavirus species.

Cowpea mild mottle virus (CpMMV) isolates identified in Florida, USA in this study are highlighted in grey. Branch support was assessed with the approximate likelihood ratio test and values >70% are shown.