Manivel Lodha      email
Institute for Virology and Immunobiology


Prof. Dr. Lars Dölken (Würzburg)
Promotion Committee:
Prof. Dr. Lars Dölken (Würzburg)
Prof. Dr. Utz Fischer (Würzburg)
Asst. Prof. Dr. Vanda Juranic Lisnic (Rijeka)
Jun. Prof. Florian Erhard (Würzburg)

Comprehensive reannotation of the human and murine cytomegalovirus genomes and characterisation of novel gene products and sORF-encoded peptides

The human cytomegalovirus (HCMV) is the largest virus known to infect humans. Both HCMV and murine cytomegalovirus (MCMV) were first sequenced over 20 years ago revealing the presence of more than 100 open reading frames (ORFs) sharing significant homology with each other. Ever since, mouse models have been utilised to better understand the pathogenesis and immune biology of CMV infections. More recently, ribosome profiling conducted for HCMV infection revealed the presence of hundreds of novel ORFs. Similar data was obtained for MCMV and a revised annotation of the coding potential for both these viruses remains missing.

In both viruses, novel ORFs mostly comprised short ORFs (sORFs) of less than 100 aa and upstream ORFs (uORFs). uORFs upstream of functional ORFs have been extensively studied as regulators of downstream ORFs which have implications in regulating stress responses in various infections. We hypothesise that the presence of viral uORFs would help the virus adapt to its cellular environment and external stimuli. A substantial portion of sORFs could code for short polypeptides which are difficult to detect by conventional techniques. Analysed MHC-I ligandomics datasets revealed the presence of sORF-encoded peptides (SEPs) that contributed to approximately 10 percent of all MHC-I associated antigens. The presence of a huge number of sORFs in CMV led us to hypothesise the potential of SEPs as novel antigens. Due to their instability and rapid degradation, these peptides are likely to be presented via direct antigen presentation, resembling the recently discovered defective ribosomal products (DRiPs). Since most T-cell responses against MCMV are primed via cross-presentation, these SEPs would form a novel class of antigens. Moreover, the presence of viral inhibitors of direct antigen presentation highlight the functional importance of such peptides.

In this project, we wish to reannotate both, the transcriptome and translatome of HCMV and MCMV using a multi-omics approach. We wish to validate the regulatory effects of various uORFs using reporter assay systems and novel genes involved in immune evasion, with a particular focus on the antigenicity of SEPs using suitable epitope tags and T-cell killing assays. Finally, we would like to analyse the protective role of these peptides in mouse models in case of MCMV and test the hypothesise of the presence of MCMV inhibitors of antigenic SEPs.