The Impact of New SARS-CoV-2 Variants on Vaccine Breakthrough: A Pilot Study on Spreading Infection in the Communities
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Abstract
Background
Coronavirus disease 2019 (COVID-19) vaccines are effective at helping protect against severe disease and death from variants; however, incident of breakthrough infection in vaccinated patients has been increased. Therefore, we aimed to assess the incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) new variants of concern in the communities and investigate vaccine breakthrough cases on our laboratory (Ayass Bioscience LLC) confirmed detection of COVID-19 variants in Dallas-Fort Worth (DFW), Texas.
Methods
Epidemiologic study has been performed at our laboratory. We studied the viral whole-genome sequence and genotyping analysis on 166 symptomatic cases of COVID-19 which were randomly selected from nasal swab positive cases assessed from June 1st to August 30th, 2021, by reverse transcription polymerase chain reaction (RT-PCR) cycle threshold (CT) values. COVID-19 variants were identified to be dominated by B.1.617.2 (89.2%) and followed by AY.3 (1.8%), B.1.1.7 (4.8%), a combination of B.1.526.1 and B.1.617.2 (3%), B.1.621 (0.6%), and P.2 (0.6%).
Result
The CT values showed significant difference among the three age groups: <30 years, 31-60 years, and >60 years by one-way ANOVA (N1: F (2, 118) =4.96, p=0.009; N2: F (2, 118) =4.95, p=0.009). No significant difference was observed by symptom, status of immunization, or vaccine manufacturer. A two-way ANOVA was performed to examine the effect of gender and variant group (Delta and other variants) on the CT values. The analyses revealed a statistically significant interaction between the effect of gender and variant group (N1, F (1.117) = 3.906, p = 0.05; N2, F (1, 117) = 7.402, p = 0.008).
Conclusion
Our study shows that Delta, the dominant variant of COVID-19, is spreading in the communities, and vaccine breakthrough cases occurred in the majority of Delta variant (91%) followed by AY.3 (5%), B.1.1.7 (2%) and 2% of the double variant of B.1.526.1 and B.1.617.2. The incidence of the breakthrough cases was not linked to a specific manufacturer. The CT value is likely to associate with age. This study also supports our laboratory’s ongoing efforts to sequence the SARS-CoV-2 virus from positive patient samples to identify the new viral variants and possible vaccine breakthrough mutations in the community.
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SciScore for 10.1101/2021.09.21.21263898: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Consent: Meanwhile, a follow-up telephone call was performed as per as oral consent form guidelines of Ayass Bioscience Laboratory to address the questions of COVID-19 immunization, travel, and positive contact history, etc. 121 of 166 cases responded to our call and completed the questionnaires. Sex as a biological variable not detected. Randomization There were 166 cases randomly selected from COVID-19 positive cases of real-time polymerase-chain-reaction (RT-PCR) assay run on the fully automated STEPONEPLUS System from Applied Biosystem. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Analyses were performed on SPSS for Windows … SciScore for 10.1101/2021.09.21.21263898: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Consent: Meanwhile, a follow-up telephone call was performed as per as oral consent form guidelines of Ayass Bioscience Laboratory to address the questions of COVID-19 immunization, travel, and positive contact history, etc. 121 of 166 cases responded to our call and completed the questionnaires. Sex as a biological variable not detected. Randomization There were 166 cases randomly selected from COVID-19 positive cases of real-time polymerase-chain-reaction (RT-PCR) assay run on the fully automated STEPONEPLUS System from Applied Biosystem. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Analyses were performed on SPSS for Windows (version 23 Inc., Chicago, IL, 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:There are some limitations in this study. First, we were unable to examine patients’ neutralizing antibody were present after the first and second dose of vaccine, or the baseline antibody test before illness and after vaccination. Second, we were unable to conduct the physical examination, blood work, or access to patients’ medical record. We are therefore unable to obtain additional information to analyze CT values and its risk factors.
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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