Role of the oral microbiome & mucosal immunity in COVID-19 disease: diagnostic/prognostic utility in South Asian populations

COVID-19 primarily infects lungs, mouth and nose, which are all mucosae (linings of body cavities) and all part of the mucosal immune system which protects mucosal surfaces and is distinct from systemic immunity. In spite of it being the primary target of the coronavirus (SARS-CoV2), its role in disease resistance, susceptibility or severity is unknown. In the UK, South Asian origin patients have a higher mortality from SARS-CoV2 infection than most ethnic groups, even after adjusting for co-morbidities, age, social gradient factors. In India, similarly adjusted mortality rates are lower than in the UK. Our hypothesis is that mucosal immunity, as reflected in the mouth nose and lungs (oral cavity/oropharynx), plays a critical role in susceptibility to, and severity of COVID-19 and explains differences in mortality between similar populations in the UK and India. We will compare mucosal and concurrent systemic immunity to reveal biomarkers for risk of disease progression which can be applied clinically so as to indicate prognosis and initiate early treatment.
COVID-19 has an initial phase of about one week when extremely high viral counts can be found in saliva and minor salivary glands, which appear to be major sites of SARS-CoV2 replication. The next phase is of increased production of non-specific immune factors (innate immunity) and especially of the products of cells (cytokines) some of which protect and others damage. It is known that 'T'-cells and cytokines are altered in both systemic and mucosal immunity to viral diseases but mucosal responses have not been much explored in relation to COVID-19.
Mucosal surfaces have their own normal fungal, bacterial and viral flora (the microbiome) which protects against unwanted pathogens. Recent years have seen great increases in our understanding of the oral microbiome in health and disease. The oral microbiome is closely related to both lung and nose microbiomes and there is evidence that upsetting the normal balance of host microbes may be a factor in COVID-19 severity. This study will therefore examine and compare the oral microbiome in two South Asian populations
Proposed Methodology: In this prospective longitudinal study, healthy controls and SARS-CoV2-positive patients of South Indian origin diagnosed to have mild or severe symptomatic disease or who have recovered from COVID will be recruited in the UK and India. Blood and saliva samples will be collected longitudinally for up to 90 days from infected individuals. The cell factors (cytokines), and different types of T cells (lymphocytes) as well as anti-SARS-CoV2 antibodies will be determined in saliva and compared with those in blood. The bacteria, fungi and viruses present in saliva (salivary microbiome) will be analysed by new molecular techniques and compared in the two populations in relation to the development of immunity and disease. We will be able to examine the development of antibodies in the mouth (reflecting those in the nose and lung), comparing those who develop mild or severe disease. We will look at the influence of pre-existing mouth disease in susceptibility to COVID. The immune responses and the oral flora will thus be correlated with COVID-19 severity as well as both COVID and non-COVID mouth disease and enable the identification of host, viral or bacterial factors which affect the susceptibility and severity of COVID in South Asian populations in the UK and India. Identification of these factors will not only reveal differences in the UK and India but will also have direct and applicable clinical benefit to both populations and others.
There are ongoing close collaborations between London, Chennai and Bangalore which should facilitate the early commencement of these studies. In London, Chennai and Bangalore, samples of blood and saliva will be taken from patients who are also part of a partner proposal (KCL-SIMS), thus enabling saving on costs of the research.

SARS-CoV2 (CoV2) primarily infects respiratory mucosae, yet the role of mucosal immunity is not known. UK South Asian (SA) patients have a higher mortality from CoV2 infection than most ethnic groups, whereas in India similarly adjusted mortality rates are lower than in the UK. We hypothesise that mucosal immunity plays a role in susceptibility to and severity of COVID-19 and explains these differences. Minor salivary glands appear to be major sites of CoV2 replication leading to extremely high viral counts in saliva and upregulated production of cytokines. Mucosal surfaces have their own microbiome which protects against pathogens and oral, lung & nasal microbiomes are closely related. Microbiome dysbiosis may be a factor in COVID-19 severity. This study will therefore compare the oral microbiome, salivary innate and specific mucosal antibody responses longitudinally among CoV2-positive SA patients in India and the UK and determine their diagnostic and prognostic utility.
Healthy controls and CoV2-positive patients of SA origin with asymptomatic or symptomatic disease or who are COVID recovered will be recruited in the UK and India. Blood and stimulated whole mouth saliva (SWMF) samples will be collected longitudinally for up to 90 days from infected individuals. Cytokines, T cell phenotypes and IgA & IgG anti-CoV2 antibodies will be determined in SWMF and compared with those in blood. The SWMF microbiome will be analysed by shotgun metagenomics and the metabolome by using NMR. The influence of pre-existing mouth disease in susceptibility to COVID will be determined. Identification of these factors should result in direct and applicable clinical benefit to SA populations and others.
Ongoing collaborations between London and Chennai will facilitate commencement of these studies. In London, samples will be taken from patients who are also part of a partner proposal (KCL-SIMS), enabling saving on research costs.