Comprehensive annotation of the Glossina pallidipes salivary gland hypertrophy virus from Ethiopian tsetse flies: a proteogenomics approach

Authors: ABD-ALLA, ADLY - International Atomic Energy Agency (IAEA); KARIITHI, HENRY - Kenya Agricultural And Livestock Research Organization; COUSSERANS, FRANCOIS - University Of Montpellier; PARKER, NICOLAS - Consultant; INCE, IKBAL - Acibadem University; Scully, Erin; BOEREN, SJEF - Wageningen University; Geib, Scott; MEKONNEN, SOLOMON - Kaliti Tsetse Mass Rearing And Irradiation Centre; VLAK, JUST - Wageningen University; PARKER, ANDREW - International Atomic Energy Agency (IAEA); VRESYEN, MARC - International Atomic Energy Agency (IAEA); BERGOIN, MAX - University Of Montpellier

Submitted to: Journal of General Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/20/2016
Publication Date: 4/1/2016
Citation: Abd-Alla, A.M., Kariithi, H.M., Cousserans, F., Parker, N.J., Ince, I.A., Scully, E.D., Boeren, S., Geib, S.M., Mekonnen, S., Vlak, J.M., Parker, A.G., Vresyen, M.J., Bergoin, M. 2016. Comprehensive annotation of the Glossina pallidipes salivary gland hypertrophy virus from Ethiopian tsetse flies: a proteogenomics approach. Journal of General Virology. 97(4):1010-1031. doi: 10.1099/igv.0.000409.

Interpretive Summary: Tsetse flies are notorious vectors of a number of human pathogens, including trypanosomes, which can cause devastating illnesses such as African sleeping sickness. To reduce incidences of tsetse fly vectored diseases, infertile male insects are often released to mate with females. Since female tsetse flies can only mate once, females that mate with a sterile male will produce no offspring. Although sterile insect technique (SIT) is a cost-effective way to reduce the population of tsetse flies, healthy insects must be reared in colony to produce suitable numbers of insects for mass release. However, Glossina pallidipes salivary gland hypertrophy virus infections can occasionally infect colonies at high levels, causing flies to develop swollen salivary glands and eventually causing mortality. For example, an SIT program was initiated to eradicate G.pallidipes from the Rift Valley of Ethiopia, however, this colony completely collapsed within two years of its establishment due to viral infection. To determine why this virus was so deadly, its genome was sequenced and genes expressed during active infection were characterized using high-throughput transcriptomics and proteomics. The viral genome associated with the Ethiopian tsetse fly colony contains more genes and numerous changes in DNA and protein sequences compared to the genomes of other salivary gland hypertrophy viruses detected in other tsetse fly colonies. This virus likely represents a new strain and the genetic differences between this strain and other previously sequenced strains possibly explain its high virulence.

Technical Abstract: The Glossina pallidipes salivary gland hypertrophy virus (GpSGHV; family Hytrosaviridae) can establish a chronic covert asymptomatic infection and an acute overt symptomatic infection in its tsetse fly host (Diptera: Glossinidae). Expression of the disease symptoms, the salivary gland hypertrophy syndrome (SGH), varies widely (10-85%) in different G.pallidipes colonies. Here, we present a comprehensive annotation of the genome of an Ethiopian GpSGHV isolate (GpSGHV-Eth) compared to the reference Ugandan GpSGHV isolate (GpSGHV-Uga; EF568108). GpSGHV-Eth has a higher SGH prevalence than GpSGHV-Uga. We show that GpSGHV-Eth genome is 190,291 bp in size, has a low G+C content (27.9%) and encodes 174 putative ORFs. By proteogenomic and transcriptome mapping, 141 and 86 ORFs were mapped by transcripts and peptides, respectively. Further, of the 174 ORFs, 132 had putative transcriptional signals (TATA-like box and poly(A) signals). Overall, 60 ORFs had both TATA-box promoters and poly(A) signals, and were mapped by both transcripts and peptides, implying that they are translated into functional proteins. Whereas GpSGHV-Eth and GpSGHV-Uga are 98.1% similar at nucleotide level, 38 ORFs in GpSGHV-Eth genome had nucleotide insertions (n=18) and deletions (n=20) compared to their GpSGHV-Uga homologs. Further, compared to the GpSGHV-Uga genome, 10 and 24 GpSGHV ORFs were deleted and novel, respectively, Proteogenomic mapping revealed that 13 core genes involved in virus replication/infection aretranslated, including three PIFs, six RNApol subunits, and LEFs 4, 5, 8 and 9. Further, 13 GpSGHV-Eth ORFs were non-canonical; they had either CTG or TTG start codons instead of ATG. Taken together, these data suggest that GpSGHV-Eth and GpSGHV-Uga represent two different lineages of the same virus. The genetic differences between GpSGHV-Eth and GpSGHV-Uga, combined with host and environmental factors possibly explain the differential GpSGHV pathogenesis observed in different G.pallidipes colonies.