Next generation sequencing of multiple SARS-CoV-2 infections in the Omicron Era
Abstract 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-...
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Nature Portfolio
2025-01-01
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| Online Access: | https://doi.org/10.1038/s41598-024-84952-6 |
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| author | Marzia Cavalli Giulia Campoli Anna Anselmo Rossella Brandi Antonella Fortunato Maria Di Spirito Anella Monte Martina Lipari Manfredo Bortone Vanessa Vera Fain Raffaele D’Amelio Florigio Lista Silvia Fillo |
| author_facet | Marzia Cavalli Giulia Campoli Anna Anselmo Rossella Brandi Antonella Fortunato Maria Di Spirito Anella Monte Martina Lipari Manfredo Bortone Vanessa Vera Fain Raffaele D’Amelio Florigio Lista Silvia Fillo |
| author_sort | Marzia Cavalli |
| collection | DOAJ |
| description | Abstract 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. |
| format | Article |
| id | doaj-art-7e54131813674bf3aa5f807349219e58 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-7e54131813674bf3aa5f807349219e582025-02-02T12:20:33ZengNature PortfolioScientific Reports2045-23222025-01-0115111410.1038/s41598-024-84952-6Next generation sequencing of multiple SARS-CoV-2 infections in the Omicron EraMarzia Cavalli0Giulia Campoli1Anna Anselmo2Rossella Brandi3Antonella Fortunato4Maria Di Spirito5Anella Monte6Martina Lipari7Manfredo Bortone8Vanessa Vera Fain9Raffaele D’Amelio10Florigio Lista11Silvia Fillo12Defence Institute for Biomedical SciencesDefence Institute for Biomedical SciencesDefence Institute for Biomedical SciencesDefence Institute for Biomedical SciencesDefence Institute for Biomedical SciencesDefence Institute for Biomedical SciencesDefence Institute for Biomedical SciencesDefence Institute for Biomedical SciencesDefence Institute for Biomedical SciencesDefence Institute for Biomedical SciencesDepartment of Clinical and Molecular Medicine, “Sapienza” University of Rome, S. Andrea University HospitalDefence Institute for Biomedical SciencesDefence Institute for Biomedical SciencesAbstract 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.https://doi.org/10.1038/s41598-024-84952-6SARS-CoV-2NGSReinfectionReactivationOmicronVaccine |
| spellingShingle | Marzia Cavalli Giulia Campoli Anna Anselmo Rossella Brandi Antonella Fortunato Maria Di Spirito Anella Monte Martina Lipari Manfredo Bortone Vanessa Vera Fain Raffaele D’Amelio Florigio Lista Silvia Fillo Next generation sequencing of multiple SARS-CoV-2 infections in the Omicron Era Scientific Reports SARS-CoV-2 NGS Reinfection Reactivation Omicron Vaccine |
| title | Next generation sequencing of multiple SARS-CoV-2 infections in the Omicron Era |
| title_full | Next generation sequencing of multiple SARS-CoV-2 infections in the Omicron Era |
| title_fullStr | Next generation sequencing of multiple SARS-CoV-2 infections in the Omicron Era |
| title_full_unstemmed | Next generation sequencing of multiple SARS-CoV-2 infections in the Omicron Era |
| title_short | Next generation sequencing of multiple SARS-CoV-2 infections in the Omicron Era |
| title_sort | next generation sequencing of multiple sars cov 2 infections in the omicron era |
| topic | SARS-CoV-2 NGS Reinfection Reactivation Omicron Vaccine |
| url | https://doi.org/10.1038/s41598-024-84952-6 |
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