Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California

doi:10.1038/s41564-021-01041-4

. 2022 Feb;7(2):277-288.

doi: 10.1038/s41564-021-01041-4. Epub 2022 Jan 10.

Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California

Venice Servellita^{1

2}, Mary Kate Morris³, Alicia Sotomayor-Gonzalez^{1

2}, Amelia S Gliwa^{1

2}, Erika Torres⁴, Noah Brazer^{1

2}, Alicia Zhou⁴, Katherine T Hernandez⁵, Madeline Sankaran⁵, Baolin Wang^{1

2}, Daniel Wong^{1

2}, Candace Wang^{1

2}, Yueyuan Zhang^{1

2}, Kevin R Reyes^{1

2}, Dustin Glasner^{1

2}, Xianding Deng^{1

2}, Jessica Streithorst^{1

2}, Steve Miller^{1

2}, Edwin Frias⁶, Mary Rodgers⁶, Gavin Cloherty⁶, John Hackett Jr⁶, Carl Hanson³, Debra Wadford³, Susan Philip⁵, Scott Topper⁴, Darpun Sachdev⁵, Charles Y Chiu^{7

8

9

10}

Affiliations

¹ Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
² UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
³ Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA.
⁴ Color Genomics, Inc., Burlingame, CA, USA.
⁵ San Francisco Department of Public Health, San Francisco, CA, USA.
⁶ Abbott Laboratories, Abbott Park, IL, USA.
⁷ Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. charles.chiu@ucsf.edu.
⁸ UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA. charles.chiu@ucsf.edu.
⁹ Department of Medicine, University of California San Francisco, San Francisco, CA, USA. charles.chiu@ucsf.edu.
¹⁰ Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA. charles.chiu@ucsf.edu.

PMID: 35013591
DOI: 10.1038/s41564-021-01041-4

Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California

Venice Servellita et al. Nat Microbiol. 2022 Feb.

. 2022 Feb;7(2):277-288.

doi: 10.1038/s41564-021-01041-4. Epub 2022 Jan 10.

Authors

Affiliations

¹ Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
² UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
³ Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA.
⁴ Color Genomics, Inc., Burlingame, CA, USA.
⁵ San Francisco Department of Public Health, San Francisco, CA, USA.
⁶ Abbott Laboratories, Abbott Park, IL, USA.
⁷ Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. charles.chiu@ucsf.edu.
⁸ UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA. charles.chiu@ucsf.edu.
⁹ Department of Medicine, University of California San Francisco, San Francisco, CA, USA. charles.chiu@ucsf.edu.
¹⁰ Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA. charles.chiu@ucsf.edu.

PMID: 35013591
DOI: 10.1038/s41564-021-01041-4

Abstract

Associations between vaccine breakthrough cases and infection by different SARS coronavirus 2 (SARS-CoV-2) variants have remained largely unexplored. Here we analysed SARS-CoV-2 whole-genome sequences and viral loads from 1,373 persons with COVID-19 from the San Francisco Bay Area from 1 February to 30 June 2021, of which 125 (9.1%) were vaccine breakthrough infections. Vaccine breakthrough infections were more commonly associated with circulating antibody-resistant variants carrying ≥1 mutation associated with decreased antibody neutralization (L452R/Q, E484K/Q and/or F490S) than infections in unvaccinated individuals (78% versus 48%, P = 1.96 × 10^-8). Differences in viral loads were non-significant between unvaccinated and fully vaccinated cases overall (P = 0.99) and according to lineage (P = 0.09-0.78). Symptomatic vaccine breakthrough infections had comparable viral loads (P = 0.64), whereas asymptomatic breakthrough infections had decreased viral loads (P = 0.023) compared with infections in unvaccinated individuals. In 5 cases with serial samples available for serologic analyses, vaccine breakthrough infections were found to be associated with low or undetectable neutralizing antibody levels attributable to an immunocompromised state or infection by an antibody-resistant lineage. Taken together, our results show that vaccine breakthrough infections are overrepresented by antibody-resistant SARS-CoV-2 variants, and that symptomatic breakthrough infections may be as efficient in spreading COVID-19 as unvaccinated infections, regardless of the infecting lineage.

Cited by

Jinhua Qinggan granules for non-hospitalized COVID-19 patients: A double-blind, placebo-controlled, and randomized controlled trial.
Shah MR, Fatima S, Khan SN, Ullah S, Himani G, Wan K, Lin T, Lau JYN, Liu Q, Lam DSC. Shah MR, et al. Front Med (Lausanne). 2022 Aug 1;9:928468. doi: 10.3389/fmed.2022.928468. eCollection 2022. Front Med (Lausanne). 2022. PMID: 35979216 Free PMC article.
Antibody affinity and cross-variant neutralization of SARS-CoV-2 Omicron BA.1, BA.2 and BA.3 following third mRNA vaccination.
Bellusci L, Grubbs G, Zahra FT, Forgacs D, Golding H, Ross TM, Khurana S. Bellusci L, et al. Nat Commun. 2022 Aug 8;13(1):4617. doi: 10.1038/s41467-022-32298-w. Nat Commun. 2022. PMID: 35941152 Free PMC article.
Pre-Omicron Vaccine Breakthrough Infection Induces Superior Cross-Neutralization against SARS-CoV-2 Omicron BA.1 Compared to Infection Alone.
da Silva ES, Kohnen M, Gilson G, Staub T, Arendt V, Hilger C, Servais JY, Charpentier E, Domingues O, Snoeck CJ, Ollert M, Seguin-Devaux C, Perez-Bercoff D. da Silva ES, et al. Int J Mol Sci. 2022 Jul 12;23(14):7675. doi: 10.3390/ijms23147675. Int J Mol Sci. 2022. PMID: 35887023 Free PMC article.
The nervous system during COVID-19: Caught in the crossfire.
Natale NR, Lukens JR, Petri WA Jr. Natale NR, et al. Immunol Rev. 2022 Jun 30:10.1111/imr.13114. doi: 10.1111/imr.13114. Online ahead of print. Immunol Rev. 2022. PMID: 35770683 Free PMC article. Review.
COVID-19 Variant Detection with a High-Fidelity CRISPR-Cas12 Enzyme.
Fasching CL, Servellita V, McKay B, Nagesh V, Broughton JP, Sotomayor-Gonzalez A, Wang B, Brazer N, Reyes K, Streithorst J, Deraney RN, Stanfield E, Hendriks CG, Fung B, Miller S, Ching J, Chen JS, Chiu CY. Fasching CL, et al. J Clin Microbiol. 2022 Jul 20;60(7):e0026122. doi: 10.1128/jcm.00261-22. Epub 2022 Jun 29. J Clin Microbiol. 2022. PMID: 35766492 Free PMC article.

See all "Cited by" articles

References

1. Baden, L. R. et al. Efficacy and safety of the mRNA-1273 SARS-CoV-2 vaccine. N. Engl. J. Med. 384, 403–416 (2021).
1. Chemaitelly, H. et al. mRNA-1273 COVID-19 vaccine effectiveness against the B.1.1.7 and B.1.351 variants and severe COVID-19 disease in Qatar. Nat. Med. https://doi.org/10.1038/s41591-021-01446-y (2021).
1. Haas, E. J. et al. Impact and effectiveness of mRNA BNT162b2 vaccine against SARS-CoV-2 infections and COVID-19 cases, hospitalisations, and deaths following a nationwide vaccination campaign in Israel: an observational study using national surveillance data. Lancet 397, 1819–1829 (2021). - DOI
1. Pilishvili, T. et al. Interim estimates of vaccine effectiveness of Pfizer-BioNTech and Moderna COVID-19 vaccines among health care personnel – 33 U.S. Sites, January–March 2021. MMWR Morb. Mortal. Wkly Rep. 70, 753–758 (2021). - DOI
1. Tang, L. et al. Asymptomatic and symptomatic SARS-CoV-2 infections after BNT162b2 vaccination in a routinely screened workforce. JAMA 325, 2500–2502 (2021). - DOI

Publication types

Actions
Actions
Actions

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions

Substances

Actions
Actions
Actions
Actions

Supplementary concepts

Actions
Actions

Grant support

LinkOut - more resources

Full Text Sources
- Nature Publishing Group
Medical
- Genetic Alliance
- MedlinePlus Health Information
Miscellaneous
- NCI CPTAC Assay Portal

[1] Baden, L. R. et al. Efficacy and safety of the mRNA-1273 SARS-CoV-2 vaccine. N. Engl. J. Med. 384, 403–416 (2021).

[2] Baden, L. R. et al. Efficacy and safety of the mRNA-1273 SARS-CoV-2 vaccine. N. Engl. J. Med. 384, 403–416 (2021).

[3] Chemaitelly, H. et al. mRNA-1273 COVID-19 vaccine effectiveness against the B.1.1.7 and B.1.351 variants and severe COVID-19 disease in Qatar. Nat. Med. https://doi.org/10.1038/s41591-021-01446-y (2021).

[4] Chemaitelly, H. et al. mRNA-1273 COVID-19 vaccine effectiveness against the B.1.1.7 and B.1.351 variants and severe COVID-19 disease in Qatar. Nat. Med. https://doi.org/10.1038/s41591-021-01446-y (2021).

[5] Haas, E. J. et al. Impact and effectiveness of mRNA BNT162b2 vaccine against SARS-CoV-2 infections and COVID-19 cases, hospitalisations, and deaths following a nationwide vaccination campaign in Israel: an observational study using national surveillance data. Lancet 397, 1819–1829 (2021). - DOI

[6] Haas, E. J. et al. Impact and effectiveness of mRNA BNT162b2 vaccine against SARS-CoV-2 infections and COVID-19 cases, hospitalisations, and deaths following a nationwide vaccination campaign in Israel: an observational study using national surveillance data. Lancet 397, 1819–1829 (2021). - DOI

[7] Pilishvili, T. et al. Interim estimates of vaccine effectiveness of Pfizer-BioNTech and Moderna COVID-19 vaccines among health care personnel – 33 U.S. Sites, January–March 2021. MMWR Morb. Mortal. Wkly Rep. 70, 753–758 (2021). - DOI

[8] Pilishvili, T. et al. Interim estimates of vaccine effectiveness of Pfizer-BioNTech and Moderna COVID-19 vaccines among health care personnel – 33 U.S. Sites, January–March 2021. MMWR Morb. Mortal. Wkly Rep. 70, 753–758 (2021). - DOI

[9] Tang, L. et al. Asymptomatic and symptomatic SARS-CoV-2 infections after BNT162b2 vaccination in a routinely screened workforce. JAMA 325, 2500–2502 (2021). - DOI

[10] Tang, L. et al. Asymptomatic and symptomatic SARS-CoV-2 infections after BNT162b2 vaccination in a routinely screened workforce. JAMA 325, 2500–2502 (2021). - DOI

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California

Affiliations

Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California

Authors

Affiliations

Abstract

Similar articles

Cited by

References

Publication types

MeSH terms

Substances

Supplementary concepts

Grant support

LinkOut - more resources

Full Text Sources

Medical

Miscellaneous

Abstract

Similar articles

Cited by

References

Publication types

MeSH terms

Substances

Supplementary concepts

Related information

Grant support

LinkOut - more resources

Full Text Sources

Medical

Miscellaneous