Next generation sequencing of multiple SARS-CoV-2 infections in the Omicron Era

Since the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the need for an effective vaccine has appeared crucial for stimulating immune system responses to produce humoral/cellular immunity and activate immunological memory. It has been demonstrated that SARS-CoV-2 variants escape neutralizing immunity elicited by previous infection and/or vaccination, leading to new infection waves and cases of reinfection. The study aims to gain into cases of reinfections, particularly infections and/or vaccination-induced protection. We conducted a retrospective descriptive study using data collected during the SARS-CoV-2 pandemic. This analysis involved Reverse Transcriptase Quantitative Polymerase Chain Reaction (RT-qPCR) and Next Generation Sequencing (NGS). RT-qPCR was performed on 416,466 naso-oropharyngeal swabs, with 10,380 samples further analyzed using NGS technology. RT-qPCR identified 350 cases of reinfection, of which 228 were subjected to detailed analysis via NGS. Our findings revealed two interesting cases involving pediatric patients who were not vaccinated. Positive results were observed in these cases within a short interval (< 60 days) and the "nature" of the infection, whether attributable to Reinfection or Viral Persistence, was investigated. Specifically, we discuss a case involving an unvaccinated 18-month-old child, which may represent one of the earliest instances of BA.5/BA.5 reinfection identified worldwide.