Distance From Drury Inn and Suites Phoenix Chandler Fashion Center to San Tan Charter School
Predominance of antibody-resistant SARS-CoV-2 variants in vaccine quantum cases from the San Francisco Bay Area, California
Abstruse
Associations between vaccine breakthrough cases and infection by SARS coronavirus 2 (SARS-CoV-2) variants take remained largely unexplored. Here we analyzed SARS-CoV-two whole-genome sequences and viral loads from 1,373 persons with COVID-19 from the San Francisco Bay Area from Feb 1 to June 30, 2021, of which 125 (9.1%) were vaccine breakthrough infections. Fully vaccinated were more than likely than unvaccinated persons to be infected past variants carrying mutations associated with decreased antibody neutralization (L452R, L452Q, E484K, and/or F490S) (78% versus 48%, p = ane.96e-08), but not past those associated with increased infectivity (L452R and/or N501Y) (85% versus 77%, p = 0.092). Differences in viral loads were non-significant between unvaccinated and fully vaccinated persons overall (p = 0.99) and according to lineage (p = 0.09 – 0.78). Viral loads were significantly higher in symptomatic as compared to asymptomatic vaccine breakthrough cases (p < 0.0001), and symptomatic vaccine quantum infections had like viral loads to unvaccinated infections (p = 0.64). In 5 cases with available longitudinal samples for serologic analyses, vaccine breakthrough infections were plant to be associated with low or undetectable neutralizing antibiotic levels attributable to immunocompromised state or infection by an antibody-resistant lineage. These findings advise that vaccine breakthrough cases are preferentially caused by circulating antibody-resistant SARS-CoV-ii variants, and that symptomatic breakthrough infections may potentially transmit COVID-nineteen as efficiently every bit unvaccinated infections, regardless of the infecting lineage.
Competing Interest Statement
C.Y.C. is the manager of the UCSF-Abbott Viral Diagnostics and Discovery Center and receives enquiry support from Abbott Laboratories, Inc. E.F. and J.H.,Jr. are employees and shareholders of Abbott Laboratories. E.T., A.Z., and South.T. are employees of Color Genomics. The other authors declare no competing interests.
Funding Statement
This work has been funded past United states CDC Epidemiology and Laboratory Capacity (ELC) for Infectious Diseases Grant six NU50CK000539 to the California Department of Public Health (M-G.Thousand., C.H., D.A.W.), the Innovative Genomics Institute (IGI) at UC Berkeley and UC San Francisco (C.Y.C.), National Institutes of Health grant R33AI129455 (C.Y.C.), US Centers for Affliction Control and Prevention contract 75D30121C10991 (C.Y.C.), and Heluna Health/California Department of Public Health contract 5NU50CK000539‐01‐12 (C.Y.C.).
Author Declarations
I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ideals committee approvals have been obtained.
Yes
The details of the IRB/oversight body that provided approval or exemption for the enquiry described are given beneath:
Remnant nasopharyngeal and/or oropharyngeal (NP/OP) samples and plasma samples from laboratory confirmed SARS-CoV-2 positive patients were retrieved from the UCSF Clinical Laboratories and stored in a biorepository until candy. Remnant samples were biobanked and retrospective medical chart review for relevant clinical and demographic metadata were performed under a waiver of consent and co-ordinate to protocols canonical by the UCSF Institutional Review Lath (protocol number x-01116, 11-05519). De-identified samples from community COVID-xix testing were obtained from Color Genomics Laboratory as part of a research collaboration. Vaccine breakthrough information corresponding to the de-identified samples from Colour Genomics were obtained from the San Francisco Department of Public Health. Approval for sequencing and analysis of these de-identified samples and metadata was obtained from the UCSF Institutional Review Board (protocol number 11-05519).
All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.
Aye
I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that whatsoever such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).
Yes
I take followed all appropriate enquiry reporting guidelines and uploaded the relevant EQUATOR Network enquiry reporting checklist(s) and other pertinent textile as supplementary files, if applicable.
Yes
Data Availability
Data Availability Assembled SARS-CoV-2 genomes in this study were uploaded to GISAID (accession numbers in Supplementary Table S2) and tin can be visualized in NextStrain. Viral genomes were also submitted to the National Center for Biotechnology Data (NCBI) GenBank database (accession numbers awaiting). Raw sequence data were submitted to the Sequence Read Annal (SRA) database. (BioProject accretion number PRJNA722044 and umbrella BioProject accretion number PRJNA171119). Code Availability FASTA files and scripting code for data analyses are available in a Zenodo data repository (https://doi.org/ten.5281/zenodo.5207242).
https://doi.org/10.5281/zenodo.5207242
Copyright
The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to brandish the preprint in perpetuity. It is made bachelor under a CC-BY-NC-ND 4.0 International license.
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