SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021
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Abstract
SARS-CoV-2 vaccination is highly effective at reducing viral infection, hospitalization and death. However, vaccine breakthrough infections have been widely observed, raising the question of whether particular viral variants or viral mutations are associated with breakthrough.
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SciScore for 10.1101/2021.10.18.21264623: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Human subjects: The University of Pennsylvania Institutional Review Board (IRB) reviewed the research protocol and deemed the limited data elements extracted with positive SARS-CoV-2 specimens to be exempt from human subject research per 45 CFR 46.104, category 4 (IRB #848605).
Consent: For hospitalized subjects at the University of Pennsylvania, following informed consent (IRB protocol #823392), patients were sampled by collection of saliva, oropharyngeal and/or nasopharyngeal swabs, or endotracheal aspirates if intubated, as previously described (33).
Field Sample Permit: Human samples were collected at Thomas Jefferson University under protocol number IRB Control # 21E.441 approved …SciScore for 10.1101/2021.10.18.21264623: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Human subjects: The University of Pennsylvania Institutional Review Board (IRB) reviewed the research protocol and deemed the limited data elements extracted with positive SARS-CoV-2 specimens to be exempt from human subject research per 45 CFR 46.104, category 4 (IRB #848605).
Consent: For hospitalized subjects at the University of Pennsylvania, following informed consent (IRB protocol #823392), patients were sampled by collection of saliva, oropharyngeal and/or nasopharyngeal swabs, or endotracheal aspirates if intubated, as previously described (33).
Field Sample Permit: Human samples were collected at Thomas Jefferson University under protocol number IRB Control # 21E.441 approved by the Thomas Jefferson University IRB.Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Remaining specimens were sequenced using the Swift Normalase® Amplicon Panels (SNAP) Core Kit along with the SARS-CoV-2 Additional Genome Coverage Primer Panel following the manufacturer’s protocol. SNAPsuggested: (SNAP, RRID:SCR_007936)Data analysis: To process sequence data, sequence reads are trimmed to remove low quality base calls (< Q20) and aligned to the original Wuhan reference sequence (NC_045512.2) with the BWA aligner tool (v0.7.17) (47), after which alignments are filtered with the Samtools package (v1.10)(48) to remove suspect alignments. BWAsuggested: (BWA, RRID:SCR_010910)Samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)Analysis code is available at http://github.com/sherrillmix/longitudinalLineages and will be deposited on Zenodo prior to final submission. Zenodosuggested: (ZENODO, RRID:SCR_004129)Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:This study has several limitations. For the vaccine breakthrough samples, we did not have paired immunological data, so it is unknown whether the vaccinations provoked protective immune responses. Our surveillance data was from a mixture of hospitalized patients, symptomatic subjects tested in clinical diagnostic laboratories, and asymptomatic subjects tested weekly at an academic institution, and so our sampling may not be entirely representative of viruses circulating in the community. Several different amplification and sequencing methods were used to acquire data. Documentation of vaccination status may be incomplete. For all the viral genome sequencing, only samples achieving a threshold level of viral RNA could be sequenced (roughly Ct <28 for swab-based testing, Ct <20 for saliva), so it is possible that other variants predominate in subjects with lower viral loads. Studies have been initiated to address some of these concerns. In summary, similar to other regions in the US and around the world, VBM/VOC and other lineages waxed and waned in the Delaware Valley, with delta lineages ultimately comprising all recent samples in the fall of 2021. Widespread vaccination was introduced in the region in winter 2020-2021, and increasing numbers of breakthrough infections have since been detected. To compare the lineages found in breakthrough with those observed in general surveillance, we introduce analysis based on Bayesian autoregressive moving average multinomial logistic re...
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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