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Jacobson KB, Pinsky BA, Montez Rath ME, Wang H, Miller JA, Skhiri M, Shepard J, Mathew R, Lee G, Bohman B, Parsonnet J, Holubar M. Post-Vaccination Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infections and Incidence of the Presumptive B.1.427/B.1.429 Variant Among Healthcare Personnel at a Northern California Academic Medical Center. Clin Infect Dis 2022; 74:821-828. [PMID: 34137815 PMCID: PMC8344553 DOI: 10.1093/cid/ciab554] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Although mRNA-based severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines report >90% efficacy, breakthrough infections occur. Little is known about their effectiveness against SARS-CoV-2 variants, including the highly prevalent B.1.427/B.1.429 variant. METHODS In this quality improvement project, we collected demographic and clinical information from post-vaccine SARS-CoV-2 cases (PVSCs), defined as healthcare personnel (HCP) with positive SARS-CoV-2 nucleic acid amplification test after receiving ≥1 vaccine dose. Available specimens were tested for L452R, N501Y, and E484K mutations using reverse-transcription polymerase chain reaction. Mutation prevalence was compared among unvaccinated, early post-vaccinated (≤14 days after dose 1), partially vaccinated (positive test >14 days after dose 1 and <14 days after dose 2), and fully vaccinated (>14 days after dose 2) PVSCs. RESULTS From December 2020 to April 2021, ≥23 090 HCP received ≥1 dose of an mRNA-based SARS-CoV-2 vaccine, and 660 HCP cases of SARS-CoV-2 occurred, of which 189 were PVSCs. Among the PVSCs, 114 (60.3%), 49 (25.9%), and 26 (13.8%) were early post-vaccination, partially vaccinated, and fully vaccinated, respectively. Of 261 available samples from vaccinated and unvaccinated HCP, 103 (39.5%), including 42 PVSCs (36.5%), had the L452R mutation presumptive of B.1.427/B.1.429. When adjusted for community prevalence of B.1.427/B.1.429, PVSCs did not have significantly elevated risk of B.1.427/B.1.429 compared with unvaccinated HCP. CONCLUSIONS Most PVSCs occurred prior to expected onset of full, vaccine-derived immunity. Presumptive B.1.427/B.1.429 was not more prevalent in post-vaccine cases than in unvaccinated SARS-CoV-2 HCP. Continued infection control measures, particularly <14 days post-vaccination, and continued variant surveillance in PVSCs are imperative to control future SARS-CoV-2 surges.
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Affiliation(s)
- Karen B Jacobson
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Benjamin A Pinsky
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Maria E Montez Rath
- Department of Medicine, Division of Nephrology, Stanford University School of Medicine, Stanford, California, USA
| | - Hannah Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Jacob A Miller
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
| | - Mehdi Skhiri
- Department of Medicine, Primary Care and Population Health, Stanford University School of Medicine, Stanford, California, USA
| | - John Shepard
- Department of Quality, Patient Safety and Clinical Effectiveness, Stanford Health Care, Stanford, California, USA
| | - Roshni Mathew
- Department of Pediatrics, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Grace Lee
- Department of Pediatrics, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Bryan Bohman
- Workforce Health and Wellness, Stanford University School of Medicine, Stanford, California, USA
| | - Julie Parsonnet
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, California, USA
| | - Marisa Holubar
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
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Deng X, Garcia-Knight MA, Khalid MM, Servellita V, Wang C, Morris MK, Sotomayor-González A, Glasner DR, Reyes KR, Gliwa AS, Reddy NP, Sanchez San Martin C, Federman S, Cheng J, Balcerek J, Taylor J, Streithorst JA, Miller S, Sreekumar B, Chen PY, Schulze-Gahmen U, Taha TY, Hayashi JM, Simoneau CR, Kumar GR, McMahon S, Lidsky PV, Xiao Y, Hemarajata P, Green NM, Espinosa A, Kath C, Haw M, Bell J, Hacker JK, Hanson C, Wadford DA, Anaya C, Ferguson D, Frankino PA, Shivram H, Lareau LF, Wyman SK, Ott M, Andino R, Chiu CY. Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant. Cell 2021; 184:3426-3437.e8. [PMID: 33991487 PMCID: PMC8057738 DOI: 10.1016/j.cell.2021.04.025] [Citation(s) in RCA: 313] [Impact Index Per Article: 104.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/02/2021] [Accepted: 04/15/2021] [Indexed: 01/07/2023]
Abstract
We identified an emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant by viral whole-genome sequencing of 2,172 nasal/nasopharyngeal swab samples from 44 counties in California, a state in the western United States. Named B.1.427/B.1.429 to denote its two lineages, the variant emerged in May 2020 and increased from 0% to >50% of sequenced cases from September 2020 to January 2021, showing 18.6%-24% increased transmissibility relative to wild-type circulating strains. The variant carries three mutations in the spike protein, including an L452R substitution. We found 2-fold increased B.1.427/B.1.429 viral shedding in vivo and increased L452R pseudovirus infection of cell cultures and lung organoids, albeit decreased relative to pseudoviruses carrying the N501Y mutation common to variants B.1.1.7, B.1.351, and P.1. Antibody neutralization assays revealed 4.0- to 6.7-fold and 2.0-fold decreases in neutralizing titers from convalescent patients and vaccine recipients, respectively. The increased prevalence of a more transmissible variant in California exhibiting decreased antibody neutralization warrants further investigation.
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Affiliation(s)
- Xianding Deng
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Miguel A Garcia-Knight
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mir M Khalid
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Candace Wang
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | | | - Alicia Sotomayor-González
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Dustin R Glasner
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Kevin R Reyes
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Amelia S Gliwa
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Nikitha P Reddy
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Claudia Sanchez San Martin
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Scot Federman
- Laboratory for Genomics Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jing Cheng
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joanna Balcerek
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jordan Taylor
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jessica A Streithorst
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Bharath Sreekumar
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Pei-Yi Chen
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Ursula Schulze-Gahmen
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Taha Y Taha
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Jennifer M Hayashi
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Camille R Simoneau
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - G Renuka Kumar
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Sarah McMahon
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Peter V Lidsky
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Peera Hemarajata
- Los Angeles County Public Health Laboratories, Downey, CA 90242, USA
| | - Nicole M Green
- Los Angeles County Public Health Laboratories, Downey, CA 90242, USA
| | - Alex Espinosa
- California Department of Public Health, Richmond, CA 94804, USA
| | - Chantha Kath
- California Department of Public Health, Richmond, CA 94804, USA
| | - Monica Haw
- California Department of Public Health, Richmond, CA 94804, USA
| | - John Bell
- California Department of Public Health, Richmond, CA 94804, USA
| | - Jill K Hacker
- California Department of Public Health, Richmond, CA 94804, USA
| | - Carl Hanson
- California Department of Public Health, Richmond, CA 94804, USA
| | - Debra A Wadford
- California Department of Public Health, Richmond, CA 94804, USA
| | - Carlos Anaya
- Monterey County Department of Public Health, Monterey, CA 93906, USA
| | - Donna Ferguson
- Monterey County Department of Public Health, Monterey, CA 93906, USA
| | - Phillip A Frankino
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Haridha Shivram
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Liana F Lareau
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Stacia K Wyman
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Melanie Ott
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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