Severe Acute Respiratory Syndrome Coronavirus 2 Delta Vaccine Breakthrough Transmissibility in Alachua County, Florida
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Abstract
Background
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant has caused a dramatic resurgence in infections in the United Sates, raising questions regarding potential transmissibility among vaccinated individuals.
Methods
Between October 2020 and July 2021, we sequenced 4439 SARS-CoV-2 full genomes, 23% of all known infections in Alachua County, Florida, including 109 vaccine breakthrough cases. Univariate and multivariate regression analyses were conducted to evaluate associations between viral RNA burden and patient characteristics. Contact tracing and phylogenetic analysis were used to investigate direct transmissions involving vaccinated individuals.
Results
The majority of breakthrough sequences with lineage assignment were classified as Delta variants (74.6%) and occurred, on average, about 3 months (104 ± 57.5 days) after full vaccination, at the same time (June-July 2021) of Delta variant exponential spread within the county. Six Delta variant transmission pairs between fully vaccinated individuals were identified through contact tracing, 3 of which were confirmed by phylogenetic analysis. Delta breakthroughs exhibited broad viral RNA copy number values during acute infection (interquartile range, 1.2-8.64 Log copies/mL), on average 38% lower than matched unvaccinated patients (3.29-10.81 Log copies/mL, P < .00001). Nevertheless, 49% to 50% of all breakthroughs, and 56% to 60% of Delta-infected breakthroughs exhibited viral RNA levels above the transmissibility threshold (4 Log copies/mL) irrespective of time after vaccination.
Conclusions
Delta infection transmissibility and general viral RNA quantification patterns in vaccinated individuals suggest limited levels of sterilizing immunity that need to be considered by public health policies. In particular, ongoing evaluation of vaccine boosters should specifically address whether extra vaccine doses curb breakthrough contribution to epidemic spread.
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SciScore for 10.1101/2021.11.10.21266134: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: The study was reviewed and approved under the category of Public Health practice by the University of Florida Institutional Review Board (IRB) and the Florida Department of Health IRB. Sex as a biological variable Relationship between VL, vaccination status and SARS-CoV-2 lineage: We performed a linear regression on the VL as dependent variable, with vaccination status (yes/no), Delta lineage (yes/no, age (<21, 21-28, 28-44, >44 years old or unknown), gender (male, female, unknown), and days from January 2021 as covariates. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Illumina’s DRAGEN pipeline was … SciScore for 10.1101/2021.11.10.21266134: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: The study was reviewed and approved under the category of Public Health practice by the University of Florida Institutional Review Board (IRB) and the Florida Department of Health IRB. Sex as a biological variable Relationship between VL, vaccination status and SARS-CoV-2 lineage: We performed a linear regression on the VL as dependent variable, with vaccination status (yes/no), Delta lineage (yes/no, age (<21, 21-28, 28-44, >44 years old or unknown), gender (male, female, unknown), and days from January 2021 as covariates. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Illumina’s DRAGEN pipeline was used to derive sample consensus sequences, which were filtered based on a minimum of 70% coverage of the genome and 20X sequencing depth. DRAGENsuggested: NonePhylogenetic tree reconstruction and optimization: Following the first in-house sequencing run and first round of BLAST protocol described above, the multiple sequence alignment for all sequences up to November 25, 2020, was used in the reconstruction of an initial maximum likelihood tree in IQ-TREE2 using the best-fit evolutionary model according to Bayesian Information Criterion 36.36. BLASTsuggested: (BLASTX, RRID:SCR_001653)Results from OddPub: Thank you for sharing your code.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.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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