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Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study.
Microbiol Spectr. 2021 12 22; 9(3):e0188221.MS

Abstract

Emergence of SARS-CoV-2 with high transmission and immune evasion potential, the so-called variants of concern (VOC), is a major concern. We describe the early genomic epidemiology of SARS-CoV-2 recovered from vaccinated health care professionals (HCP). Our postvaccination COVID-19 symptoms-based surveillance program among HCPs in a 17-hospital network identified all vaccinated HCPs who tested positive for COVID-19 after routine screening or after self-reporting. From 1 January 2021 to 30 April 2021, 23,687 HCPs received either mRNA-1273 or BNT162b2 mRNA vaccine. All available postvaccination SARS-CoV-2 samples and a random collection from nonvaccinated patients during the similar time frame were subjected to VOC screening and whole-genome sequencing (WGS). Sixty-two percent (23,697/37,500) of HCPs received at least one vaccine dose, with 60% (22,458) fully vaccinated. We detected 138 (0.58%, 138/23,697) COVID-19 cases, 105 among partially vaccinated and 33 (0.15%, 33/22,458) among fully vaccinated. Five partially vaccinated required hospitalization, four with supplemental oxygen. VOC screening from 16 fully vaccinated HCPs identified 6 (38%) harboring N501Y and 1 (6%) with E484K polymorphisms; percentage of concurrent nonvaccinated samples was 37% (523/1,404) and 20% (284/1,394), respectively. There was an upward trend from January to April for E484K/Q (3% to 26%) and N501Y (1% to 49%). WGS analysis from vaccinated and nonvaccinated individuals indicated highly congruent phylogenies. We did not detect an increased frequency of any receptor-binding domain (RBD)/N-terminal domain (NTD) polymorphism between groups (P > 0.05). Our results support robust protection by vaccination, particularly among recipients of both doses. Despite VOCs accounting for over 40% of SARS-CoV-2 from fully vaccinated individuals, the genomic diversity appears to proportionally represent VOCs among nonvaccinated populations. IMPORTANCE A number of highly effective vaccines have been developed and deployed to combat the COVID-19 pandemic. The emergence and epidemiological dominance of SARS-CoV-2 mutants with high transmission potential and immune evasion properties, the so-called variants of concern (VOC), continue to be a major concern. Whether these VOCs alter the efficacy of the administered vaccines is of great concern and a critical question to study. We describe the initial genomic epidemiology of SARS-CoV-2 recovered from partial/fully vaccinated health care professionals and probe specifically for VOC enrichment. Our findings support the high level of protection provided by full vaccination despite a steep increase in the prevalence of polymorphisms associated with increased transmission potential (N501Y) and immune evasion (E484K) in the nonvaccinated population. Thus, we do not find evidence of VOC enrichment among vaccinated groups. Overall, the genomic diversity of SARS-CoV-2 recovered postvaccination appears to proportionally represent the observed viral diversity within the community.

Authors+Show Affiliations

Mailman School of Public Health, Columbia Universitygrid.21729.3f Irving Medical Center, New York, New York, USA.Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA. Hackensack Meridian School of Medicine, Nutley, New Jersey, USA.Hackensack Meridian Health Biorepository, Hackensack, New Jersey, USA.Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA. Hackensack Meridian School of Medicine, Nutley, New Jersey, USA.New York Genome Centergrid.429884.b, New York, New York, USA.Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA.Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA.Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA.Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA.New York Genome Centergrid.429884.b, New York, New York, USA.New York Genome Centergrid.429884.b, New York, New York, USA.New York Genome Centergrid.429884.b, New York, New York, USA.Hackensack Meridian Health Biorepository, Hackensack, New Jersey, USA.Hackensack Meridian Health BI Analytics, Edison, New Jersey, USA.Hackensack Meridian Health BI Analytics, Edison, New Jersey, USA.John Theurer Cancer Center, Outcomes Division, Hackensack University Medical Centergrid.239835.6, Hackensack, New Jersey, USA.John Theurer Cancer Center, Outcomes Division, Hackensack University Medical Centergrid.239835.6, Hackensack, New Jersey, USA.New York Genome Centergrid.429884.b, New York, New York, USA.Hackensack Meridian Health Biorepository, Hackensack, New Jersey, USA.Hackensack Meridian Health Biorepository, Hackensack, New Jersey, USA.New York Genome Centergrid.429884.b, New York, New York, USA.Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA. Hackensack Meridian School of Medicine, Nutley, New Jersey, USA.Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

34787439

Citation

Mathema, Barun, et al. "Postvaccination SARS-COV-2 Among Health Care Workers in New Jersey: a Genomic Epidemiological Study." Microbiology Spectrum, vol. 9, no. 3, 2021, pp. e0188221.
Mathema B, Chen L, Chow KF, et al. Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. Microbiol Spectr. 2021;9(3):e0188221.
Mathema, B., Chen, L., Chow, K. F., Zhao, Y., Zody, M. C., Mediavilla, J. R., Cunningham, M. H., Composto, K., Lee, A., Oschwald, D. M., Germer, S., Fennessey, S., Patel, K., Wilson, D., Cassell, A., Pascual, L., Ip, A., Corvelo, A., Dar, S., ... Kreiswirth, B. N. (2021). Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. Microbiology Spectrum, 9(3), e0188221. https://doi.org/10.1128/Spectrum.01882-21
Mathema B, et al. Postvaccination SARS-COV-2 Among Health Care Workers in New Jersey: a Genomic Epidemiological Study. Microbiol Spectr. 2021 12 22;9(3):e0188221. PubMed PMID: 34787439.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. AU - Mathema,Barun, AU - Chen,Liang, AU - Chow,Kar Fai, AU - Zhao,Yanan, AU - Zody,Michael C, AU - Mediavilla,Jose R, AU - Cunningham,Marcus H, AU - Composto,Kaelea, AU - Lee,Annie, AU - Oschwald,Dayna M, AU - Germer,Soren, AU - Fennessey,Samantha, AU - Patel,Kishan, AU - Wilson,David, AU - Cassell,Ann, AU - Pascual,Lauren, AU - Ip,Andrew, AU - Corvelo,André, AU - Dar,Sophia, AU - Kramer,Yael, AU - Maniatis,Tom, AU - Perlin,David S, AU - Kreiswirth,Barry N, Y1 - 2021/11/17/ PY - 2021/11/18/pubmed PY - 2022/1/6/medline PY - 2021/11/17/entrez KW - COVID-19 KW - SARS-CoV-2 KW - breakthrough KW - spike protein KW - vaccine KW - variants of concern SP - e0188221 EP - e0188221 JF - Microbiology spectrum JO - Microbiol Spectr VL - 9 IS - 3 N2 - Emergence of SARS-CoV-2 with high transmission and immune evasion potential, the so-called variants of concern (VOC), is a major concern. We describe the early genomic epidemiology of SARS-CoV-2 recovered from vaccinated health care professionals (HCP). Our postvaccination COVID-19 symptoms-based surveillance program among HCPs in a 17-hospital network identified all vaccinated HCPs who tested positive for COVID-19 after routine screening or after self-reporting. From 1 January 2021 to 30 April 2021, 23,687 HCPs received either mRNA-1273 or BNT162b2 mRNA vaccine. All available postvaccination SARS-CoV-2 samples and a random collection from nonvaccinated patients during the similar time frame were subjected to VOC screening and whole-genome sequencing (WGS). Sixty-two percent (23,697/37,500) of HCPs received at least one vaccine dose, with 60% (22,458) fully vaccinated. We detected 138 (0.58%, 138/23,697) COVID-19 cases, 105 among partially vaccinated and 33 (0.15%, 33/22,458) among fully vaccinated. Five partially vaccinated required hospitalization, four with supplemental oxygen. VOC screening from 16 fully vaccinated HCPs identified 6 (38%) harboring N501Y and 1 (6%) with E484K polymorphisms; percentage of concurrent nonvaccinated samples was 37% (523/1,404) and 20% (284/1,394), respectively. There was an upward trend from January to April for E484K/Q (3% to 26%) and N501Y (1% to 49%). WGS analysis from vaccinated and nonvaccinated individuals indicated highly congruent phylogenies. We did not detect an increased frequency of any receptor-binding domain (RBD)/N-terminal domain (NTD) polymorphism between groups (P > 0.05). Our results support robust protection by vaccination, particularly among recipients of both doses. Despite VOCs accounting for over 40% of SARS-CoV-2 from fully vaccinated individuals, the genomic diversity appears to proportionally represent VOCs among nonvaccinated populations. IMPORTANCE A number of highly effective vaccines have been developed and deployed to combat the COVID-19 pandemic. The emergence and epidemiological dominance of SARS-CoV-2 mutants with high transmission potential and immune evasion properties, the so-called variants of concern (VOC), continue to be a major concern. Whether these VOCs alter the efficacy of the administered vaccines is of great concern and a critical question to study. We describe the initial genomic epidemiology of SARS-CoV-2 recovered from partial/fully vaccinated health care professionals and probe specifically for VOC enrichment. Our findings support the high level of protection provided by full vaccination despite a steep increase in the prevalence of polymorphisms associated with increased transmission potential (N501Y) and immune evasion (E484K) in the nonvaccinated population. Thus, we do not find evidence of VOC enrichment among vaccinated groups. Overall, the genomic diversity of SARS-CoV-2 recovered postvaccination appears to proportionally represent the observed viral diversity within the community. SN - 2165-0497 UR - https://www.unboundmedicine.com/medline/citation/34787439/Postvaccination_SARS_COV_2_among_Health_Care_Workers_in_New_Jersey:_A_Genomic_Epidemiological_Study_ L2 - https://doi.org/10.1128/Spectrum.01882-21 DB - PRIME DP - Unbound Medicine ER -