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To respond rapidly to emerging threats, it is critical to understand the pathogen itself. ³Ô¹ÏºÚÁÏ researchers are working in basic discovery science to explore the biology and transmission of emerging infections. Using our specialised expertise and infrastructure, ³Ô¹ÏºÚÁÏ researchers are perfecting testing concepts, designs, and technologies, for example, new methods of virus culture, that can be quickly deployed against new threats.

³Ô¹ÏºÚÁÏ’s strengths in molecular and basic virology lie in specialist:

• Expertise, e.g., virology, in the handling of airborne and blood-borne pathogens, quantitative proteomics and glycomics, risk assessment of new variants, established in vivo methods for transmission, and deep mutational screening
• Infrastructure, e.g. specialist containment facilities for in vivo and in vitro studies

Experts working in this area

• : Molecular virology; real-time characterisation of pathogenesis and transmission of viruses, including influenza, avian flu  (H5N1); risk assessment of zoonotic and pandemic threats; exchanging global knowledge of variants; recombinant virology. Examples (in Covid): Real-time characterisation of SARS-CoV-2 and variants; Exchanging global knowledge to enable in-country risk assessment of SARS-CoV-2 variants
• : Vascular pathology; mediators of vascular damage, vascular inflammation and thrombosis.
• : Structural glycomics and glycobiology; characterisation of influenza glycan receptors. Example (in Covid): Site-specific characterisation of SARS-CoV-2 spike glycoprotein receptor-binding.
• : Virus genomics, including HIV and influenza, MERS, ebola. Example (in Covid): Deep mutagenesis scanning  of SARS-CoV-2. Influenza example: Identified the first human influenza disease severity determining allele in people hospitalised with pandemic influenza A H1N1.
• : Identification of virus-host interactions that influence the outcome of dengue, Zika, and West Nile virus infection.
• Bioinformatics, viral genomics.
• : Molecular basis of infection-induced cardiac and lung damage and systemic response; myocarditis; using in vitro systems to assess viral damage to cardiomyocytes and endothelial cells. Example (in Covid): Understanding cellular and molecular changes that occur within tissues and systemically (PBMCs).
• : Pathogenic mechanisms of virus-related inflammation of the respiratory tract, using recombinant and natural variants of viruses.
• : Respiratory and transplant medicine.
• : Renal and transplant pathology; understanding vascular injury and thrombosis. 
• Mechanisms of mucosal infection.
• : Human challenge studies, infection transmission, including via ferret-ferret transmission models. Example (in Covid): ATACCC SARS-CoV-2 household transmission study; SARS-CoV-2 transmission in households, including in vaccinated people.
• : Genomics and molecular epidemiology, including for S. pyogenes and scarlet fever; role of toxins in perpetuating outbreaks; emergent lineages. Example (in Covid): Biomarkers of infection and routes of SARS-CoV2 transmission.
• : Interactions between emerging viruses and innate immune system related to emerging virus transmission, pandemic potential, and pathogenesis. Example (in Covid): Evolution of enhanced innate immune evasion by SARS-CoV-2.
• : Phylogenetic analysis and methods.

Infrastructure and networks

• Department of Infectious Disease facilities, including large suite containing eight CL3 laboratories, one CL2 laboratory, two ISO class 7 cleanrooms
• Centre for Immunology and Vaccinology CL3 Cell Sorting Facility
• NIHR Health Protection Research Unit in Respiratory Infections
• Glycobiology Network
• Glycosciences Laboratory