Investigation of Symptomatic SARS-CoV-2 Reinfection Cases Among Healthcare Workers at La Rabta University Hospital
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| author | Ben Halima, Meriam Abbes, Salma Dallagi, Amani khouja, nihel Ismail, Saloua Baraketi, Emna Ben Jemaa, Abdelmajid Hsinet, Jihen Battikh, Hajer Benzarti, Aida Zribi, Meriam |
| author_facet | Ben Halima, Meriam Abbes, Salma Dallagi, Amani khouja, nihel Ismail, Saloua Baraketi, Emna Ben Jemaa, Abdelmajid Hsinet, Jihen Battikh, Hajer Benzarti, Aida Zribi, Meriam |
| contents | <p><strong><span>Introduction:</span></strong><span><br>The 2019 coronavirus (COVID-19) epidemic began in December 2019 in Wuhan, China, and rapidly spread worldwide, becoming a major public health threat. The aim of our study was, on the one hand, to investigate the genomic characteristics of the SARS-CoV-2 virus in 35 isolated viral particles, and on the other hand, to describe the epidemiological and clinical features of patients who were infected at least twice with the virus within La Rabta University Hospital (CHU La Rabta).</span></p> <p><strong><span>Materials and Methods:</span></strong><span><br>Nasopharyngeal swabs were collected at CHU La Rabta, and all patients who experienced reinfection and/or long COVID were included in the study. Molecular diagnosis of SARS-CoV-2 was carried out in two steps: viral RNA was extracted using the alphaPrep™ Viral DNA/RNA Extraction Kit (ALPHAGENE, Korea) with the NG-15 PLUS automatic extractor (France), followed by viral RNA identification via qRT-PCR on Rotor-Gene Q (Qiagen, Germany) or DLAB Accurate 96 Real-Time PCR (YIMA, China), targeting the ORF1ab and nucleocapsid (N) genes.</span></p> <p><span>Whole genome sequencing (WGS) was performed on only thirty-five viral particles collected during different periods and waves of the COVID pandemic. Sequencing was carried out using the iSeq 100 system (2x150bp) (Illumina, USA). The obtained sequences were analyzed using the DRAGEN RNA Pathogen Detection Pipeline and the DNA Explify Respiratory Virus Oligos Panel Platform available on the BaseSpace Sequence Hub (https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub.html).</span></p> <p><strong><span>Results and Discussion:</span></strong><span><br>Between November 20, 2020, and August 18, 2022, a total of 234 nasopharyngeal samples tested positive, corresponding to 113 patients who experienced at least two episodes of COVID-19, among whom 25 were healthcare workers at CHU La Rabta. During our study, only 4 patients were classified as having long COVID, based on CDC criteria, and all healthcare staff included showed reinfection.</span></p> <p><span>The mean age of patients was 40.58 ± 10.52 years, with a clear female predominance (78.76%). The reinfection rate increased over time and across pandemic waves, reaching 15.04% during the 6th wave. WGS revealed sequences ranging in size from 29,440 to 29,823 bp, with coverage between 71% and 99%. Analysis of sequenced genomes showed a marked predominance of the Omicron variant (97%), which was the emerging variant during this phase of the pandemic. One sequence from November 2021 corresponded to the B.1.617.2 (Delta) variant. Among the Omicron samples: 7 belonged to subvariant BA.5, 6 to BA.1, 17 to BA.2, and one to the recombinant XAD. Finally, three distinct recombinants (FL.25, GS.7, and EG.4.5) were identified during 2023.</span></p> <p><span>For a single patient who was infected three times, the variants from the second and third reinfections (considered as long COVID, lasting 40 days) were sequenced and identified as two distinct Omicron subvariants (BA.5 and BA.5.2).</span></p> <p><span><strong>Conclusion:</strong></span></p> <p><span>Our study highlights the importance of WGS, which remains a key tool for monitoring the evolution of the virus. It enables the detection of emerging variants, assessment of their potential impact on transmissibility, virulence, and immune escape, and guides vaccination and therapeutic strategies.</span></p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_15690712 |
| institution | Zenodo |
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| publishDate | 2025 |
| publisher | Zenodo |
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| spellingShingle | Investigation of Symptomatic SARS-CoV-2 Reinfection Cases Among Healthcare Workers at La Rabta University Hospital Ben Halima, Meriam Abbes, Salma Dallagi, Amani khouja, nihel Ismail, Saloua Baraketi, Emna Ben Jemaa, Abdelmajid Hsinet, Jihen Battikh, Hajer Benzarti, Aida Zribi, Meriam <p><strong><span>Introduction:</span></strong><span><br>The 2019 coronavirus (COVID-19) epidemic began in December 2019 in Wuhan, China, and rapidly spread worldwide, becoming a major public health threat. The aim of our study was, on the one hand, to investigate the genomic characteristics of the SARS-CoV-2 virus in 35 isolated viral particles, and on the other hand, to describe the epidemiological and clinical features of patients who were infected at least twice with the virus within La Rabta University Hospital (CHU La Rabta).</span></p> <p><strong><span>Materials and Methods:</span></strong><span><br>Nasopharyngeal swabs were collected at CHU La Rabta, and all patients who experienced reinfection and/or long COVID were included in the study. Molecular diagnosis of SARS-CoV-2 was carried out in two steps: viral RNA was extracted using the alphaPrep™ Viral DNA/RNA Extraction Kit (ALPHAGENE, Korea) with the NG-15 PLUS automatic extractor (France), followed by viral RNA identification via qRT-PCR on Rotor-Gene Q (Qiagen, Germany) or DLAB Accurate 96 Real-Time PCR (YIMA, China), targeting the ORF1ab and nucleocapsid (N) genes.</span></p> <p><span>Whole genome sequencing (WGS) was performed on only thirty-five viral particles collected during different periods and waves of the COVID pandemic. Sequencing was carried out using the iSeq 100 system (2x150bp) (Illumina, USA). The obtained sequences were analyzed using the DRAGEN RNA Pathogen Detection Pipeline and the DNA Explify Respiratory Virus Oligos Panel Platform available on the BaseSpace Sequence Hub (https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub.html).</span></p> <p><strong><span>Results and Discussion:</span></strong><span><br>Between November 20, 2020, and August 18, 2022, a total of 234 nasopharyngeal samples tested positive, corresponding to 113 patients who experienced at least two episodes of COVID-19, among whom 25 were healthcare workers at CHU La Rabta. During our study, only 4 patients were classified as having long COVID, based on CDC criteria, and all healthcare staff included showed reinfection.</span></p> <p><span>The mean age of patients was 40.58 ± 10.52 years, with a clear female predominance (78.76%). The reinfection rate increased over time and across pandemic waves, reaching 15.04% during the 6th wave. WGS revealed sequences ranging in size from 29,440 to 29,823 bp, with coverage between 71% and 99%. Analysis of sequenced genomes showed a marked predominance of the Omicron variant (97%), which was the emerging variant during this phase of the pandemic. One sequence from November 2021 corresponded to the B.1.617.2 (Delta) variant. Among the Omicron samples: 7 belonged to subvariant BA.5, 6 to BA.1, 17 to BA.2, and one to the recombinant XAD. Finally, three distinct recombinants (FL.25, GS.7, and EG.4.5) were identified during 2023.</span></p> <p><span>For a single patient who was infected three times, the variants from the second and third reinfections (considered as long COVID, lasting 40 days) were sequenced and identified as two distinct Omicron subvariants (BA.5 and BA.5.2).</span></p> <p><span><strong>Conclusion:</strong></span></p> <p><span>Our study highlights the importance of WGS, which remains a key tool for monitoring the evolution of the virus. It enables the detection of emerging variants, assessment of their potential impact on transmissibility, virulence, and immune escape, and guides vaccination and therapeutic strategies.</span></p> |
| title | Investigation of Symptomatic SARS-CoV-2 Reinfection Cases Among Healthcare Workers at La Rabta University Hospital |
| url | https://doi.org/10.5281/zenodo.15690712 |