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Research Fellow in metagenomics (Lecturer grade) 

Former European Academy of Allergy and Clinical Immunology (EAACI) elected Junior member- Systems Medicine and Omics Working Group (www.eaaci.org)

Research interests

My research primarily focuses on the identification of respiratory tract virus species using sequencing-based metagenomics. The respiratory tract is a major gateway of infections mainly due to the environmental exposures. It is currently thought that when a virus encounters a mucosal surface, the interplay between viral invasion and host antiviral defence is the one determining the severity and outcome of the infection. However, recent advances in virus detection techniques draw a new context, uncovering the presence of  highly circulating mucosal viruses whose potential effect on the course of infection is currently unknown. In this picture, multiple indigenous vira species and viral genome sequences constitute a pool of virus-derived stimuli with no apparent (asymptomatic or subsymptomatic) clinical relevance. An updated technical and conceptual approach is needed to investigate acute respiratory viral infections. This should integrate state of the art viromics and systems medicine approaches with the aim to define factors which determine viral pathogenesis within the context of the pathobiome i.e. the interaction amongst pathogen-host-virome. First we want to describe the respiratory virome during homeostasis (health) and identify its properties (structural and functional). Then we wish to monitor their alterations during an acute viral infection and finally investigate their differential expression in allergic respiratory diseases such as asthma.The respiratory virome is in a dynamic state and its’ alterations are able to describe the susceptibility of a host to viral and bacterial infections, the context and nature of the host-microbe interaction, and the pathogenicity of an offending virus. Identifying factors which determine viral load, its clinical relevance and the pertinent disease outcomes, is an important pursuit as it can lead to novel diagnostic and therapeutic approaches for respiratory pathologic conditions.

I am also interested in the evolution of the Human rhinovirus genome during in vitro and in vivo infections. Our aim is to construct evolutionary models based on data produced from in vitro infection of multiple human epithelial cell lines and primary cells. We wish to extend this into different allergic diseases in order to identify how a specific tissue niche pushes towards specific evolution patterns and vice versa. We recently secured an Institutional Strategic Support Fund (ISSF) in collaboration with Wellcome Trust to address the above aims (RED). 

For opportunities in MSc and PhD projects please contact me at spyridon.megremis@manchester.ac.uk

My collaborations

Memberships of committees and professional bodies


Bsc (Hons) in Molecular Genetics

PhD Medical Genetics


Methodological knowledge



Molecular genetics

Epithelial cell cultures

Virus propagation and in vitro infections


Gene expression assays


Expertise related to UN Sustainable Development Goals

In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This person’s work contributes towards the following SDG(s):

  • SDG 3 - Good Health and Well-being


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