Genomic, immunological, and clinical analysis of COVID‐19 vaccine breakthrough infections in Beijing, China
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Abstract
As the coronavirus disease 2019 (COVID‐19) pandemic is still ongoing and severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) variants are circulating worldwide, an increasing number of breakthrough infections are being detected despite the good efficacy of COVID‐19 vaccines. Data on 88 COVID‐19 breakthrough cases (breakthrough infections group) and 41 unvaccinated cases (unvaccinated group) from June 1 to August 22, 2021, were extracted from a cloud database established at Beijing Ditan Hospital to evaluate the clinical, immunological, and genomic characteristics of COVID‐19 breakthrough infections. Among these 129 COVID‐19 cases, 33 whole genomes were successfully sequenced, of which 23 were Delta variants, including 15 from the breakthrough infections group. Asymptomatic and mild cases predominated in both groups, but two patients developed severe disease in the unvaccinated group. The median time of viral shedding in the breakthrough infections group was significantly lower than that in the unvaccinated group ( p = 0.003). In the breakthrough infections group, the IgG titers showed a significantly increasing trend ( p = 0.007), and the CD4 + T lymphocyte count was significantly elevated ( p = 0.018). For people infected with the Delta variant in the two groups, no significant difference was observed in either the quantitative reverse‐transcription polymerase chain reaction results or viral shedding time. In conclusion, among vaccinated patients, the cases of COVID‐19 vaccine breakthrough infections were mainly asymptomatic and mild, IgG titers were significantly increased and rose rapidly, and the viral shedding time was shorter.
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SciScore for 10.1101/2021.11.17.21266499: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Ethical approval: The study was approved by the Institutional Review Board of Beijing Ditan Hospital, Capital Medical University in Beijing (approval number JDLY2020-020-01). Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Antibodies Sentences Resources Corresponding serum samples were tested for anti-SARS-CoV-2 antibodies using a chemiluminescence immunoassay (CLIA; Bioscience, Chongqing, China). anti-SARS-CoV-2suggested: NoneSoftware and Algorithms Sentences Resources The viral RNA was extracted using Kingfisher Flex Purification System (ThermoFisher, Waltham, MA, USA), and Libraries were prepared using a … SciScore for 10.1101/2021.11.17.21266499: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Ethical approval: The study was approved by the Institutional Review Board of Beijing Ditan Hospital, Capital Medical University in Beijing (approval number JDLY2020-020-01). Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Antibodies Sentences Resources Corresponding serum samples were tested for anti-SARS-CoV-2 antibodies using a chemiluminescence immunoassay (CLIA; Bioscience, Chongqing, China). anti-SARS-CoV-2suggested: NoneSoftware and Algorithms Sentences Resources The viral RNA was extracted using Kingfisher Flex Purification System (ThermoFisher, Waltham, MA, USA), and Libraries were prepared using a Nextera XT Library Prep Kit (Illumina, San Diego, CA, USA), and the resulting DNA libraries were sequenced on a MiniSeq platform (Illumina) using a 300-cycle reagent kit. MiniSeqsuggested: NoneWhole-genome sequence alignment was conducted using the Muscle tool in MEGA (v7.0). Musclesuggested: (MUSCLE, RRID:SCR_011812)MEGAsuggested: (Mega BLAST, RRID:SCR_011920)Statistical analysis: The statistical analyses were performed using SPSS version 25.0 (SPSS IBM, Armonk, NY, USA). SPSSsuggested: (SPSS, RRID:SCR_002865)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:This study had some limitations. There were relatively few cases in the unvaccinated group, and most patients did not have full genome sequencing results, which may be related to the low viral load (high CT value) in some patients which were tested negative in the origin country. In addition, the number of patients that had breakthrough infections after being vaccinated with non-inactive vaccines was much lower than the number of patients vaccinated with inactive vaccines. Being vaccinated does not mean we can throw caution to the wind and put ourselves and others at risk, mainly because the research is still ongoing into how much vaccines protect against disease, infection, and viral transmission. Therefore, for the foreseeable future, we still need to continue wearing masks and washing our hands, and we need to ensure good indoor ventilation, continue physical distancing, and continue avoiding crowds.
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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