HYBRID EVENT: You can participate in person at Rome, Italy or Virtually from your home or work.

4th Edition of World Congress on Infectious Diseases

June 21-22, 2023 | Rome, Italy

June 21 -22, 2023 | Rome, Italy
Infection 2023

Valeria Di Lollo

Speaker at World Congress on Infectious Diseases 2023 - Valeria Di Lollo
Istituto Zooprofilattico Sperimentale (IZS), Italy
Title : SARS-CoV-2 lineage identification from massive parallel sequencing data: An analytical workflow


Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of the ongoing outbreak of the disease known as coronavirus disease 2019 (COVID-19). The genetic plasticity of SARS-CoV-2 has determined the emergence of numerous variants with enhanced adaptive capacity, infectiousness, and spread through the population. In this context, sequencing of the whole SARS-CoV-2 genome, using next-generation sequencing (NGS) platforms, is a powerful method for monitoring viral genome evolution. However, rigorous validation studies are needed to optimize the labor-intensive workflows and the sequencing data analysis pipelines. Therefore, in this study, we evaluated the accuracy and sensitivity of an NGS-based method for identifying variants of SARS-CoV-2 in nasopharyngeal swab samples. The method comprises two sequential parts: a wet laboratory section to prepare the NGS libraries using a commercial kit (Illumina COVIDSeq Test), and a dry computational section consisting of a bioinformatics pipeline to analyze the NGS data and determine the SARS-CoV-2 lineage. Our results suggest that the method can properly detect the lineage until very low viral levels. The lineage call was negatively affected in samples with the lowest viral load, which presented percentages of horizontal coverage much lower than the reference value (95 %) and a high number of unassigned nucleotides in the consensus sequence (N). In these samples, we identified the limit of detection (LOD) corresponding to real-time RT-PCR Ct values ranging from 32 to 35 (1.6 to 2.3 genomic copies/μl). In conclusion, in this study, we evaluated the opportunity to use an NGS-based method to monitor the evolution of variants in the SARS-CoV-2 genome, and we concluded that the use of the COVIDSeq Test kit is powerful for genomic surveillance of SARS-CoV-2. Moreover, identifying parameters such as accuracy, sensitivity, and repeatability can help the scientific community to develop rigorous validation studies, which are crucial for improving the application of the NGS technology to COVID-19 control strategies.
Audience Take Away:
• The presentation could help the audience to improve understanding on how to quickly detect the presence of SARS-CoV-2 for diagnostic and researcher purposes;
• It could facilitate the researchers to extend further NGS-based validation studies, essentials to improve COVID-19 control strategies;
• It could help the audience to comprehend the importance of combining conventional (RTPCR) and high-throughput approaches for the detection of SARS-CoV-2 in clinical samples.


Valeria Di Lollo graduated with an MS in Reproductive Biotechnologies degree course in 2015 at the University of Teramo, Italy. She received her PhD degree in 2020 at the Istituto Zooprofilattico Sperimentale (IZS) dell’ Abruzzo e Molise “G. Caporale” with a dissertation on the application of RNA-sequencing technology for the genomic characterization of ovine epithelial amniotic stem cells. Since 2021, she works within the research group supervised by Dr. Cesare Cammà head of the “National Reference Centre for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis” at the Istituto Zooprofilattico Sperimentale (IZS) dell’ Abruzzo e Molise “G. Caporale”.