Researchers from the ibs.GRANADA validate a technique that accelerates the massive diagnosis of COVID19 by PCR

According to a study coordinated by the Instituto de Investigación Biosanitaria ibs.GRANADA at the Hospital Universitario de Clínico San Cecilio de Granada, the grouping of samples or pooling improves the efficiency in the diagnosis of SARS COV-2 infection.

The antiretroviral resistance research group of the ibs.GRANADA has coordinated, together with the Microbiology group of the University Hospital of Santiago de Compostela, a multicenter study that consists of analyzing the samples collected nasopharyngeally by groups, with the intention of increasing the efficiency of diagnosis for SARS COV-2 infection. The technique, called pooling, involves processing groups of samples, rather than individual samples, using Real Time PCR.

In this study, 342 groups of 10 individual samples and 11 groups of 9 individual samples were processed, finding that 253 groups (2519 samples) were negative and 99 groups (990 samples) were positive. The total of positive samples was 241 samples, only 6,85% of all study participants, so this pooling strategy would have saved 2167 PCR tests.

This technique has proven to be very efficient, but when the prevalence is very high it is not as useful to determine the infection by SARS COV-2. It is only optimal to use it when the population prevalence does not exceed 10%. In this way, the size of the pool, that is, of the grouping, will depend on the incidence that exists at that moment.

This research, led by Dr. Federico García, principal investigator of the group and Microbiologist at the Hospital Universitario Clínico San Cecilio, has shown high efficiency in the diagnosis with the grouping of samples compared to individual analysis, demonstrating in all cases a excellent performance in terms of sensitivity, specificity and predictive ability whether the result is positive or negative.

At this time the current incidence in Granada is less than 10%, so pools of 10 individual samples can be made. In this way, the processing capacity of the samples by PCR to obtain results can be increased up to 10 times.

This work, in which samples from more than 3.500 patients have been used, has been published in one of the most prestigious journals in Microbiology, Clinical Microbiology and Infection, located in the top ten in the world ranking of the specialty.

The results of this study contribute to increasing the capacity to carry out determinations in laboratories, it becomes a very useful tool in the diagnosis and screening of different groups, especially for the care of the most vulnerable people and those considered essential.

About the Research Group

The antiretroviral resistance research group of the ibs.GRANADA, led by Dr. Federico García who develops his work in the Microbiology Unit of the San Cecilio Clinical University Hospital of Granada, coordinates the Spanish Network for HIV Research on subtypes and resistance and collaborates with several European organizations on HIV resistance (ESAR-SPREAD, Eurocord-CHAIN, EuRESIST-INTEGRATE) and hepatitis resistance (SHARED, HEPCARE). He has actively participated in a recent investigation on resistance to drugs transmitted in Spain and Europe, in genotypic investigation of HIV viral tropism, in the clinical importance of low and very low level viremia of HIV and in the molecular epidemiology of HIV to guide public health interventions. The group also actively participates in hepatitis C virus research, coordinating various activities in the GEHEP (Spanish Group for the Study of Viral Hepatitis of the Spanish Society of Clinical Microbiology and Infectious Diseases), and is coordinator of HEPCRESP, the national cohort Spanish for resistance of HCV to new DAAs. The group is also on the Steering Committee for HEPCARE (Europe) and SHARED (Global) hepatitis.

Bibliographic reference

Sample pooling for SARS-CoV-2 RT-PCR screening

Adolfo de Salazar, Antonio Aguilera, Rocio Trastoy, Ana Fuentes, Juan Carlos Alados, Manuel Causse, Juan Carlos Galán, Antonio Moreno, Matilde Trigo, Mercedes Pérez-Ruiz, Carolina Roldán, Maria José Pena, Samuel Bernal, Esther Serrano-Conde, Gema Barbeito, Eva Torres, Cristina Riazzo, Jose Luis Cortes-Cuevas, Natalia Chueca, Amparo Coira, Juan Manuel Sanchez- Calvo, Eduardo Marfil, Federico Becerra, María José Gude, Ángeles Pallarés, María Luisa Pérez Del Molino, Federico García,

Clinical Microbiology and Infection (2020). Volume 26, Issue 12.

https://doi.org/10.1016/j.cmi.2020.09.008.