Genome Interactions During COVID-19 Infections

Laboratory Study

SARS-Cov2 and its consequences

In December 2019, several cases of a new respiratory illness were described in Wuhan, China. By January 2020, it was confirmed that these infections were caused by a novel coronavirus, which was subsequently named SARS-CoV2, while the disease is called COVID-19. The COVID-19 pandemic has caused considerable morbidity and mortality and caused long-term health effects, which have not been assessed yet.

In this regard, the AGYA working group Health and Society identified the importance of knowing how the viral, human, and bacterial genomes interact among affected individuals. The clinical manifestations of the disease caused by the virus vary in severity, ranging from no or mild symptoms to rapid progression to respiratory failure. However, since the knowledge on the viral genome already paved the way to the implementation of diagnostic, therapeutic and preventive means, the bacterial profiles of the affected individuals are not well studied yet and may act as additional risk factor for the severity of the disease. The intensity of response might be also related to genetic variations in the human genome that vary from one population to another and will also be part of this study, which aims to characterize the three core elements of this respiratory infection – the pathogen (SARS-CoV-2), the airway microbiome, and the human host response. This new information will be applied to facilitate a better understanding and diagnosis of COVID-19 in North Africa.

COVID-19 in Tunisia

Tunisia is the second most affected country in Africa considering the total COVID-19 mortality rate. Therefore, the AGYA working group Health and Society sees an urgent need to investigate the strains involved in COVID-19 in order to better understand the susceptibility factors of a SARS-CoV-2 infection and transcriptomic patient responses. 

Gathering Arab and German expertise

In this project, AGYA members Prof. Dr. Lilia Romdhane and Dr. Olfa Messaoud sequenced the viral, human, and bacterial transcriptomes in 28 COVID-19 patients from Tunisia through a metatranscriptomic analysis at Institut Pasteur de Tunis. Dr. Shadi Albarqouni employed AI algorithms to analyze medical imaging data of these patients to complement the metatranscriptomic sequencing data. Dr. Mohammad Adm conducted the entire statistical data analysis. The clinical, pharmacological, and anthropological interpretation of the data were supported by the expertise of Dr. Suhair Sunoqrot and Dr. Laila Prager, respectively.  All research efforts followed the purpose to identify the factors and underlying mechanisms that drive the most severe form of the disease and facilitate a better understanding and diagnosis of COVID-19. The working group met regularly online to discuss the progress and results of the project, and prepares currently a research publication.