PED-COVID_Infect

COVID-19 represents an unprecedented world-wide challenge due to the transmissibility of the virus, its impact on morbidity and mortality, the uncertainty regarding the development of long-term immunity, and the current paucity of efficient therapeutic options. Understanding the kinetics of shedding of Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2), and the duration of viral infectivity is of critical importance for controlling the pandemic. Such understanding is most crucial for the patients experiencing an asymptomatic or pauci-symptomatic infection as a large proportion of transmissions appears to occur from these subjects. Very few studies investigated the duration of detection of viral RNA in asymptomatic or pre-symptomatic subjects, and more specifically in children. They suggest that the presence of infectious virus is correlated to the overall viral load and inversely correlated with the delay from symptoms onset and the appearance of a neutralizing antibody response. Other factors that could have an impact on infectivity duration are still uncertain. This includes the innate and the adaptive immune response to SARS-CoV-2 as well as the concomitant presence of other viruses which can elicit cross-immunity. In particular, the impact of prior immunity to SARS-CoV-2 or to seasonal coronaviruses on the duration of SARS-CoV-2 infectivity warrants to be explored further. The objective of the PED-COVID_Infect project is to measure SARS-CoV-2 infectivity in a cohort of pauci-symptomatic children and their parents to evaluate how the duration and intensity of infectious virus shedding are affected by viral and immune interference, in comparison to adults. The project will benefit from the unique longitudinal collection of nasopharyngeal, saliva and blood samples from the PED-COVID cohort currently implemented in children and adults undergoing asymptomatic or pauci-symptomatic SARS-CoV-2 infection, already funded by a PHRC. We will determine the kinetics of viral clearance by assessing SARS-CoV-2 virus load and viability in the upper respiratory airways and the saliva, and its modulation by 4 main factors: (i) anti-SARS-CoV-2 antibody response at the local and general level; (ii) pre-existing antibodies towards seasonal coronaviruses; (iii) co-infections with specific respiratory pathogenic viruses; (iv) composition of the whole local eucaryotic virome. Virological characterization will be based on RT-PCR for quantification, RNA sequencing and virus infectivity on VeroE6 cells. Anti-SARS-CoV-2 and seasonal coronavirus virus antibodies will be assessed in serum by a liquid-phase Luciferase Immunoprecipitation System (LIPS)-based assay and in the saliva and the nasopharyngeal mucosa by ELISA. NGS-based agnostic metagenomics will focus on the whole viral population of the nasopharyngeal mucosa. The outcomes of our project, which combines virological, serological and metagenomic data, will provide a better understanding of the duration of SARS-CoV-2 infectivity in pauci-symptomatic children and adults, as well as new insights as to factors that could modulate virus infectivity. Such knowledge is key to inform public health policy, including quarantine, isolation and contact tracing.