Previous works and international experience
Due to its reduced costs and its accessibility by hospitals, genomic sequencing is considered a valuable tool for healthcare and public health.
One of the activities in which it has shown its usefulness has been in monitoring and responding to epidemics on the ground and in real time (1).
During the Ebola epidemic in West Africa in 2014, the sequencing of 98 samples of the virus were very useful to know the spread of the disease and take action quickly (2).
For the rapid response in public health to COVID-19, the genomic sequencing of the virus may be even more useful since sequencing tests are affordable both in terms of price and speed, due to the small size of its genome (30Kb).
In a recent study of local outbreaks of COVID-19 in China, the sequencing of the virus genome and the use of bioinformatic analysis has provided information, available within 48 hours, of great use for epidemiological surveillance and decision-making (3). Other larger studies in China show how the epidemic wave itself masks smaller waves with differentiated genetic characteristics, allowing us to observe the shape of diffusion of the epidemic at the local level, and the impact of travel limitations (4).
The phylogenetic analysis of a reduced set of sequences from local outbreaks in the USA has demonstrated the routes of diffusion, but it does not fully explain the role of local transmission compared to imported cases, making clear the need to incorporate genomic sequencing in a systematic way at the local level (5).
Along the same lines and in order to support the public health response to COVID-19, in the United Kingdom they have started a project aimed at sequencing all samples positive for SARS-Cov-2. On the other hand, it is known that a series of genes have effects both on the virus (activating or deactivating it), and on the patient, in terms of his susceptibility or symptoms (for example, genes related to cytokine storms (6)).
Therefore, the knowledge of the genetic variability of individuals will be another key piece to understand the COVID-19 epidemic and make clinical decisions with patients.
Local situation
In spite of a widespread dissemination of the virus, the incidence of the disease is very uneven in the territory of Andalusia. Nearby provinces such as Granada and Almería present the greatest interprovincial differences (rates of 151 and 45 per 100,000 inhabitants respectively).
The differences are greater between other territories (rate of 241 in the Granada District and 30 in Córdoba-Guadalquivir). There are also great differences between nearby areas such as Córdoba-Norte and Córdoba-Guadalquivir (157 compared to 30) or Sierra de Huelva and Sierra Norte de Sevilla (106 compared to 41).
On the other hand, apart from the personal characteristics already known that influence the evolution of the disease, we find unique patients whose disease evolution is different from the dominant pattern. We know the personal characteristics of the patients, their environment and their clinical situation, with special groups such as health workers, the place of infection, with special situations in residence for the erderly and other centers such as hospitals, with great variability. Differences in spread, incidence, symptoms, and response to drugs may be related to viral genetics, patient genetics or a combination of both.
The genomic sequence of the virus is a key element to anticipate the spread of the disease and for decision-making in Public Health.
It will help to understand its role in the different forms of disease presentation, and from the point of view of clinical decisions, will help to detect and use as biomarkers the genomic characteristics of the virus that will provide relevant information on the spread, the severity of the symptoms or the response to treatments.
However, genomic data without clinical and epidemiological information are of very limited utility. For this reason, this project also makes use of the advantage offered by the Andalusian health system, with its universal electronic health history and epidemiological information of the System of Epidemiological Surveillance of Andalusia, which can be enriched with data from the Population Health database (BPS) (7).
These resources offer the possibility of dynamically linking the symptoms and evolution of patients and their response to treatment with the genomic sequences of the viruses that were isolated from them. In this sense, the possibility of having a set of genomic data on viruses supplemented with clinical information on the evolution of their disease makes this project unique and allows it to quickly obtain prognostic biomarkers and response to treatment that can be immediately used both within the project and be extended to the rest of the health system quickly.
In addition, this project will lay the foundations for the use of genomic sequencing as a methodology that can be routinely incorporated into epidemiological surveillance and decision-making in the health system (8).
1. Molster, C.M., Bowman, F.L., Bilkey, G.A., Cho, A.S., Burns, B.L., Nowak, K.J. and Dawkins, H.J. (2018) The evolution of public health genomics: exploring its past, present, and future. Frontiers in public health, 6, 247.
2. Gire, S.K., Goba, A., Andersen, K.G., Sealfon, R.S., Park, D.J., Kanneh, L., Jalloh, S., Momoh, M., Fullah, M. and Dudas, G. (2014) Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. science, 345, 1369-1372.
3. Volz, E., Fu, H., Wang, H., Xi, X., Chen, W., Liu, D., Chen, Y., Tian, M., Tan, W. and Zai, J. (2020) Genomic epidemiology of a densely sampled COVID19 outbreak in China. medRxiv.
4. Lu, J., Plessis, L.d., Liu, Z., Hill, V., Kang, M., Lin, H., Sun, J., Francois, S., Kraemer, M.U.G., Faria, N.R. et al. (2020) Genomic epidemiology of SARS-CoV-2 in Guangdong Province, China. medRxiv, 2020.2004.2001.20047076.
5. Fauver, J.R., Petrone, M.E., Hodcroft, E.B., Shioda, K., Ehrlich, H.Y., Watts, A.G., Vogels, C.B.F., Brito, A.F., Alpert, T., Muyombwe, A. et al. (2020) Coast-to-coast spread of SARS-CoV-2 in the United States revealed by genomic epidemiology. medRxiv, 2020.2003.2025.20043828.
6. Mehta, P., McAuley, D.F., Brown, M., Sanchez, E., Tattersall, R.S. and Manson, J.J. (2020) COVID-19: consider cytokine storm syndromes and immunosuppression. The Lancet, 395, 1033-1034.
7. Muñoyerro-Muñiz, D., Goicoechea-Salazar, J.A., García-León, F.J., Laguna-Téllez, A., Larrocha-Mata, D. and Cardero-Rivas, M. (2019) Conexión de registros sanitarios: base poblacional de salud de Andalucía. Gaceta Sanitaria, In press.
8. Gardy, J.L. and Loman, N.J. (2018) Towards a genomics-informed, real-time, global pathogen surveillance system. Nature Reviews Genetics, 19, 9.
