Implementing personalized medicine in Covid19 included developing actions to define by means of BD and AI the interaction of genomics, epigenetics, metagenomics and viral sequencing in the development of events such as infection, severe disease, response to treatment and response to vaccination. A joint instruction was carried out on January 2020 from the General Secretariat for Research, Development and Innovation in Health and the Management Directorate of the Andalusian Health Service for the Management of samples in the approach to Personalized Medicine in COVID-19. Healthcare professionals will also have access to SARS-CoV-2 virus complete sequencing study by electronic biochemical request (MPA). The San Cecilio Clinical Hospital for Eastern Andalusia and Virgen del Rocio University Hospital for Western Andalusia were established as reference centers for receiving viral samples (
Figure 1A) and sequencing them, respectively (
Figure 1B), and the Bioinformatics Area process sequencing data (
Figure 1C), joint with COVID registry metadata (
Figure 1D), previously collected from the Hospitals (
Figure 1E), and reporting back relevant epidemiological information to the COVID registry (
Figure 1F) and information on lineages and variants to the Hospitals for supporting clinical decisions (
Figure 1G). As previously stated, the clinical data of the Andalusian Health System is stored in the BPS (
Figure 1H), but in this case, viral genomes are also stored in BPS (
Figure 1I) linked to the rest of the patient’s clinical data, offering an unprecedented opportunity for large-scale secondary studies and implementation in clinical practice (
Figure 1). Finally, the Bioinformatics Area submits the viral sequences to the ENA database, which is available to the scientific community. Since February, more than 2000 whole viral genomes have been sequenced, allowing the construction of a resource that depicts the evolution of SARS-CoV-2 along time and across the geography of Andalusia
[6]. This systematic genomic surveillance system has allowed following the increase of the B.1.1.7 since February to become a majority or to detect new VOCs, such as the Brazilian lineage P1 or the South African B.1.351, and VOIs such as the Ugandan variant A.23.1 or others.
Figure 1. Circuit for COVID19 genomic surveillance. (
A) Two reference Hospitals, San Cecilio and Virgen del Rocio, collect SARS-CoV-2 samples from Eastern and Western Andalusia, respectively. (
B) Samples are sent to GENYO or IBIS sequencing facilities. (
C) Sequencing data are sent to the Bioinformatics Area for processing and (
D) linking to metadata from the COVID registry, (
E) previously collected from the Hospitals. (
F) Bioinformatics reports relevant epidemiological information to the COVID registry and (
G) information on lineages and variants to the Hospitals for supporting clinical decisions. (
H) Clinical data on COVID-19 patients recorded in the Hospitals is stored in the BPS. (
I) Viral genomes are also stored in BPS linked to the rest of the patient’s clinical data for further secondary use.
3. Concluding Remarks
The pandemic has pushed us to a new scenario promoting association and relationship between governments and the scientific community at the same time that emerged multidisciplinary teams to take care of this complex disease together with telemedicine to guarantee health care keeping at home. Deep sequencing, bioinformatic area and clinicians working on personalized medicine could help to better understand the interaction between the virus and the host. These tools should be available for physicians able to include in their everyday decision-making process. The increasing need for personalized medicine supported by scientific and objective data, big data and AI systems to create algorithms based on individual variables (genomic), the host and the guest (pathogen and patient subject). Public and private investment for the generation and transfer of knowledge could support the development of high-quality translational and collaborative research to face a threatening situation similar to this terrible pandemic.