Molecular, Immunological, and Clinical Characterization of SARS-CoV-2 Infection in Breakthrough-Infected Healthcare Workers During the LastWave of The Pandemic in Shiraz, Iran

The coronavirus disease 2019 (COVID-19) poses a threat to the global economy and public health. Mutations in the spike protein of the virus can impact the functional characteristics and effectiveness of vaccines.

This study aimed to analyze mutations in three key regions of the spike protein, investigate clinical presentations, and assess protective immune levels in healthcare workers (HCWs) who had received full vaccine doses but were re-infected.

In this cross-sectional study, 49 breakthrough-infected HCWs were included from November 2021 to May 2022. After confirming COVID-19 reinfection, the SARS-CoV-2 genome was extracted using the ROJE extraction kit, and genetic variation analysis was performed through Sanger sequencing. Blood samples were collected with prior consent, and ELISA tests were performed to determine antibody levels. Clinical presentations were recorded, and independent t-tests revealed no significant gender-based differences in the C-terminal point mutation.

In this study, 75.5% (37/49) of the included HCWs were female (P-value < 0.05), and 25 were qualified for PCR and gene sequencing. Mutations were observed in 25, 10, and 1 sequence(s) of the C-terminal domain, N-terminal domain, and RBD regions of the S1 gene, respectively. The mutations had no significant correlation with the patient’s gender, age, or occupation, but they were significantly more prevalent in those with underlying diseases. 63.3% (31/49) of patients had high or very high IgG levels, and none had undetectable antibody levels at the time of reinfection. Loss of the sense of smell (69.4% - 34/49), sore throat (65.3% - 32/49), headache (59.2% - 29/49), and cough (57.1% - 28/49) were the most prevalent clinical manifestations (P > 0.05) in breakthrough-infected HCWs, aligning with the pattern of symptoms seen in the Omicron wave. However, the loss of the sense of taste showed significant results concerning clinical manifestation (P < 0.05). The examination of mutations revealed the presence of the Omicron variant in the majority of individuals. Point mutations in the C-terminal region did not significantly vary based on age, gender, or vaccine type. No significant difference was observed between vaccine types and clinical symptoms.

In conclusion, this study identified spike protein mutations in reinfections among vaccinated healthcare workers. While mutations were prevalent, no significant correlations were found with demographics or vaccine types. Symptoms resembled the Omicron variant, notably with the loss of the sense of taste as a significant marker. Detectable antibody levels post-reinfection suggest that vaccine-induced immunity remains robust. Continuous monitoring of virus variants is crucial for optimizing vaccination strategies in the face of evolving strains.