The immune response to COVID-19 is thought to be dysregulated across the spectrum of disease. It is therefore important to both understand aspects of immune response that lead to protective immunity as well as identify characteristics within the adaptive immune system that may correlate to disease severity. Only by understanding these various aspects can we determine how best to drive impact towards improving both prevention and care. Our on-going studies are focused on evaluating the B cell repertoire across the disease spectrum to understand how the set-point and longitudinal changes in this compartment influence response to infection as well as the potential response to future anti-viral therapies.

Coronavirus Disease 19 (COVID-19) is a respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has grown to a worldwide pandemic with substantial mortality. Immune mediated damage has been proposed as a pathogenic factor, but immune responses in lungs of COVID-19 patients remain poorly characterized. Therefore we conducted transcriptomic, histologic and cellular profiling of post mortem COVID-19 (n=34 tissues from 16 patients) and normal lung tissues (n=9 tissues from 6 patients). Two distinct immunopathological reaction patterns of lethal COVID-19 were identified. One pattern showed high local expression of interferon stimulated genes (ISGhigh) and cytokines, high viral loads and limited pulmonary damage, the other pattern showed severely damaged lungs, low ISGs (ISGlow), low viral loads and abundant infiltrating activated CD8+ T cells and macrophages. ISGhigh patients died significantly earlier after hospitalization than ISGlow patients. Our study may point to distinct stages of progression of COVID-19 lung disease and highlights the need for peripheral blood biomarkers that inform about patient lung status and guide treatment.

Integrated approach of virus sequencing and host genetics in a Covid-19 North Portuguese cohort Available high-throughput tools are powerful in unveiling the biological mechanisms governing host-pathogen interactions, as the half-year investigation in the context of Covid-19 is demonstrating. We are analysing 250 complete SARS-CoV-2 sequences (Ion AmpliSeq SARS-CoV-2 Research Panel) obtained from North Portuguese patients, including 24 individuals in one of the first transmission chains. This chain was supposedly initiated by a 50–years old male who travelled to Italy (on the 19th February 2020) accompanied by two work colleagues (one belonging to his family). The viral sequences elucidated that the supposedly patient 0 bears a 20B strain, but the remaining screened individuals who met him at a party (23rd February 2020) and other work colleagues were affiliated with a 20A strain. We are now focusing on the mutations, trying to disentangling the timeline within the transmission chain. We will present time-series viral sequencing data for an extremely long (97 days) shedding COVID-19 case. We will relate RT-qPCR CT value with the quantification through the TapeStation System (Agilent Technologies), SARS-CoV-2 quasispecies detected and in vitro culture, in order to provide insights into infectivity capacity along time. Finally, we will discuss how to design an informative genome-wide association host genetics strategy. We have confirmed that samples originally extracted for diagnostic purposes (extracted with kits for viral detection, without DNAse treatment) can also be directly used with the Applied Biosystems Axiom genotyping system. A careful selection of the control group is essential to empower the statistic resolution of the test.

The application of next-generation sequencing to interrogate immune repertoires and methods in which these highly complex datasets can be mined to examine immune regulation and/or identify potential biomarkers has evolved considerably over the years. With advances in sequencing technologies and development of comprehensive, intuitive analysis tools, NGS-based repertoire analysis has become more accessible to the broader research community. Thermo Fisher Scientific’s streamlined and user-friendly TCR and BCR sequencing laboratory and analysis pipelines enable just about anyone to incorporate this powerful tool into their research program.

In this discussion, we present examples of how repertoire analysis can be used to answer different types of research questions. Summaries of different studies leveraging TCR and BCR sequencing in human disease research to better understand mechanisms involved in inflammatory diseases are presented. Methods of experimental design, sequencing, and analysis are introduced for each, with examples of figures that can be generated with the user-friendly analysis portal.

The SARS-CoV-2 virus has impacted billions of lives globally and has spurred many scientists to address the biggest questions regarding this novel coronavirus in their research. Researchers have taken on the initiative to understand the transmission of this virus and host response as well as identify potential future treatments and develop potential future therapies, including vaccines. In this webinar, we review some of these key areas of research and explore the potential impact that the gut microbiome has on host response to SARS-CoV-2 as well as the efficacy of various immune interventions such as future vaccines.