Genome Analysis of a Glossina pallidipes Salivary Gland Hypertrophy Virus Reveals a Novel, Large, Double-Stranded Circular DNA Virus

Abstract

Several species of tsetse flies can be infected by the Glossina pallidipes salivary gland hypertrophy virus (GpSGHV). Infection causes salivary gland hypertrophy and also significantly reduces the fecundity of the infected flies. To better understand the molecular basis underlying the pathogenesis of this unusual virus, we sequenced and analyzed its genome. The GpSGHV genome is a double-stranded circular DNA molecule of 190,032 bp containing 160 nonoverlapping open reading frames (ORFs), which are distributed equally on both strands with a gene density of one per 1.2 kb. It has a high A؉T content of 72%. About 3% of the GpSGHV genome is composed of 15 sequence repeats, distributed throughout the genome. Although sharing the same morphological features (enveloped rod-shaped nucleocapsid) as baculoviruses, nudiviruses, and nimaviruses, analysis of its genome revealed that GpSGHV differs significantly from these viruses at the level of its genes. Sequence comparisons indicated that only 23% of GpSGHV genes displayed moderate homologies to genes from other invertebrate viruses, principally baculoviruses and entomopoxviruses. Most strikingly, the GpS-GHV genome encodes homologues to the four baculoviral per os infectivity factors (p74 [pif-0], pif-1, pif-2, and pif-3). The DNA polymerase encoded by GpSGHV is of type B and appears to be phylogenetically distant from all DNA polymerases encoded by large double-stranded DNA viruses. The majority of the remaining ORFs could not be assigned by sequence comparison. Furthermore, no homologues to DNA-dependent RNA polymerase subunits were detected. Taken together, these data indicate that GpSGHV is the prototype member of a novel group of insect viruses.

Two viruses that cause salivary gland hypertrophy in Glossina pallidipes and Musca domestica are related and form a distinct phylogenetic clade

“…In MdSGHV, the 4 mer TAAG motif was strongly overrepresented in the 100 and 200 bp sequences upstream of the identified ORFs and could represent a viral gene promoter motif (Table 3, Supplementary Table S1 available in JGV Online). The TAAG motif was also strongly represented in the GpSGHV upstream regions of identified ORFs (Abd-Alla et al, 2008). This TAAG motif is ubiquitously found in promoters of baculovirus late genes (Table 3) and is known to be the canonical sequence to initiate baculovirus late transcripts (Blissard & Rohrmann, 1990).…”

“…All putative ORFs identified in GpSGHV (GenBank accession no. EF568108) (Abd-Alla et al, 2008) and MdSGHV (GenBank accession no. EU522111) (Garcia-Maruniak et al, 2008) were compared to the GenBank protein database using the National Center for Biotechnology Information BLAST searches (Altschul et al, 1990(Altschul et al, , 1997, including the non-redundant standard protein-protein BLAST (BLASTP) searches for viruses (taxid 10239).…”

“…Both viruses have a circular dsDNA genome (Abd-Alla et al, 2008;Garcia-Maruniak et al, 2008). The GpSGHV genome is 65 753 bp longer than the MdSGHV genome with 52 more putative ORFs and a much lower G+C content (Table 1).…”

“…The genome sequences from GpSGHV (Abd-Alla et al, 2008) and MdSGHV (Garcia-Maruniak et al, 2008) show that they were not closely related to any other large entomopathogenic DNA viruses available in the current databases. In this study, we analyse these two viruses and compare the extent of homology between the ORFs, the putative promoter regions, the genome collinearity, and phylogenetic relatedness of the two SGHVs to each other and to other large invertebrate DNA viruses.…”

Nudivirus Genomics and Phylogeny

“…Besides in nudiviruses, homologues to baculovirus core genes were also detected in two salivary gland hypertrophy viruses (SGHVs) MdSGHV infecting the house fly Musca domestica and GpSGHV infecting the tsetse fly Glossina pallidipes (Abd-Alla et al 2008, Garcia-Maruniak et al 2008. GpSGHV and MdSGHV share 37 homologous ORFs and are phylogenetically closely related (Garcia-Maruniak et al 2009).…”