Cold case: The disappearance of Egypt bee virus, a fourth distinct master strain of deformed wing virus linked to honeybee mortality in 1970's Egypt

Abstract

In 1977, a sample of diseased adult honeybees (Apis mellifera) from Egypt was found to contain large amounts of a previously unknown virus, Egypt bee virus, which was subsequently shown to be serologically related to deformed wing virus (DWV). By sequencing the original isolate, we demonstrate that Egypt bee virus is in fact a fourth unique, major variant of DWV (DWV-D): more closely related to DWV-C than to either DWV-A or DWV-B. DWV-A and DWV-B are the most common DWV variants worldwide due to their close relationship and transmission by Varroa destructor. However, we could not find any trace of DWV-D in several hundred RNA sequencing libraries from a worldwide selection of honeybee, varroa and bumblebee samples. This means that DWV-D has either become extinct, been replaced by other DWV variants better adapted to varroa-mediated transmission, or persists only in a narrow geographic or host range, isolated from common bee and beekeeping trade routes.

Keywords: Apis mellifera; Bioinformatic screening; Deformed wing virus; Egypt bee virus; Honeybee; Master strain; RNA sequencing; Varroa destructor; Western blot.

Fig. 1

Genome organization and phylogenetic analyses (2 columns). A Map of the DWV-D genome showing the location and size of the major genomic regions: 5’ UTR and 3’ UTR (yellow), Lp gene (red), capsid proteins VP1, VP2, VP3 and VP4 (blue), and the non-structural proteins (green), including the helicase, VPg, 3C-protease and RdRp genes. Shown above the genome map are the conserved protease cleavage sites for DWV-A, DWV-B, DWV-C, DWV-D, and Darwin bee virus-3 for processing the polyprotein into functional units. B Plot of the nucleotide similarity between DWV-D and either DWV-A (black), DWV-B (red) or DWV-C (blue) across a sliding 200 bp window. C Phylogenetic relationships between the four major DWV variants relative to the closest known outgroup (Darwin bee virus 3) for the four major genomic regions: UTR (yellow), Lp gene (red), structural proteins (blue), and non-structural proteins (green) based on either the nucleotide sequence (left) or the amino acid sequence (right). The number of characters included in each phylogram is shown in Additional file 1: Table S2. The phylogenetic trees with the highest log likelihood (see Additional file 1: Table S2) are shown. All trees are drawn to scale, with branch lengths measured in the number of substitutions (nucleotide or amino acid) per site. The degree of confidence in the branching nodes, based on bootstrapping the alignment 500 times, is shown by the solid, shaded, and white circles. Nodes with less than 70% bootstrap support (no circle) are unreliable

Fig. 2

Host and geographic origin of screened samples (2 columns). Map showing the geographic and host origins of the samples and RNA sequencing libraries screened for the presence of DWV-D. Major host groups (Apis, Bombus, Varroa) and whether or not the samples come from areas free of varroa are represented by different colors. The number of unique SRAs of each type in each location is indicated by the size of the marker. The MENA samples screened by Sanger sequencing ([27]; Additional file 1: Fig. S2) are bounded by a red circle