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Wen Z, Yuan Y, Zhao Y, Wang H, Han Z, Li M, Yuan J, Sun C. Enhancement of SARS-CoV-2 N Antigen-Specific T Cell Functionality by Modulating the Autophagy-Mediated Signal Pathway in Mice. Viruses 2023; 15:1316. [PMID: 37376617 DOI: 10.3390/v15061316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/28/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
The frequent SARS-CoV-2 variants have caused a continual challenge, weakening the effectiveness of current vaccines, and thus it is of great importance to induce robust and conserved T cellular immunity for developing the next-generation vaccine against SARS-CoV-2 variants. In this study, we proposed a conception of enhancing the SARS-CoV-2 specific T cell functionality by fusing autophagosome-associated LC3b protein to the nucleocapsid (N) (N-LC3b). When compared to N protein alone, the N-LC3b protein was more effectively targeted to the autophagosome/lysosome/MHC II compartment signal pathway and thus elicited stronger CD4+ and CD8+ T cell immune responses in mice. Importantly, the frequency of N-specific polyfunctional CD4+ and CD8+ T cells, which can simultaneously secrete multiple cytokines (IFN-γ+/IL-2+/TNF-α+), in the N-LC3b group was significantly higher than that in the N alone group. Moreover, there was a significantly improved T cell proliferation, especially for CD8+ T cells in the N-LC3b group. In addition, the N-LC3b also induced a robust humoral immune response, characterized by the Th1-biased IgG2a subclass antibodies against the SARS-CoV-2 N protein. Overall, these findings demonstrated that our strategy could effectively induce a potential SARS-CoV-2 specific T cellular immunity with enhanced magnitude, polyfunctionality, and proliferation, and thus provided insights to develop a promising strategy for the design of a novel universal vaccine against SARS-CoV-2 variants and other emerging infectious diseases.
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Affiliation(s)
- Ziyu Wen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Yue Yuan
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Yangguo Zhao
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Haohang Wang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Zirong Han
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Minchao Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Jianhui Yuan
- Nanshan District Center for Disease Control and Prevention, Shenzhen 518000, China
| | - Caijun Sun
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
- Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou 510080, China
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Clinical features and severe outcome predictors of COVID-19 vaccine breakthrough infection among hospitalized patients: results from Egypt severe acute respiratory infections sentinel surveillance, 2021-2022. BMC Infect Dis 2023; 23:130. [PMID: 36879217 PMCID: PMC9987052 DOI: 10.1186/s12879-023-08097-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 02/17/2023] [Indexed: 03/08/2023] Open
Abstract
BACKGROUND COVID-19 vaccines are effective against infections and outcomes; however, breakthrough infections (VBT) are increasingly reported, possibly due to waning of vaccine-induced immunity or emerging variants. Most studies have focused on determining VBT rate based on antibody levels. This study aims at describing clinical features, risks, time trends, and outcomes of COVID-19 VBT among hospitalized patients in Egypt. METHODS Data of SARS-CoV-2 confirmed patients hospitalized in 16 hospitals was obtained from the severe acute respiratory infections surveillance database, September 2021-April 2022. Data includes patients' demographics, clinical picture, and outcomes. Descriptive analysis was performed and patients with VBT were compared to not fully vaccinated (UPV). Bivariate and multivariate analyses were performed using Epi Info7 with a significance level < 0.05 to identify VBT risk factors. RESULTS Overall, 1,297 patients enrolled, their mean age 56.7 ± 17.0 years, 41.5% were males, 64.7% received inactivated, 25.% viral vector, and 7.7% mRNA vaccine. VBT was identified in 156(12.0%) patients with an increasing trend over time. VBT significantly was higher in (16-35 years) age, males, in those who received inactivated vaccine compared to corresponding groups of UPV (14.1 vs. 9.0%, p < 0.05 and 57.1 vs. 39.4%, p < 0.001 and 64.7 vs. 45.1, p < 0.01 respectively). Whereas receiving mRNA vaccine was significantly protective against VBT (7.7 vs. 21.6%, p < 001). VBT patients tend to have shorter hospital stays and lower case fatality (mean hospital days = 6.6 ± 5.5 vs. 7.9 ± 5.9, p < 0.01 and CFR = 28.2 vs. 33.1, p < 0.01 respectively). MVA identified younger ages, male gender, and inactivated vaccines as risks for VBT. CONCLUSION The study indicated that COVID-19 vaccines significantly reduce hospital days and fatality. VBT trend is on the rise and males, young ages, and inactivated vaccine receivers are at higher risk. Caution regarding relaxation of personal preventive measures in areas with higher or increasing incidences of COVID-19, particularly for the at-risk group even if they are vaccinated. The vaccination strategy should be revised to reduce VBT rate and increase vaccine effectiveness.
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Tisler A, Stirrup O, Pisarev H, Kalda R, Meister T, Suija K, Kolde R, Piirsoo M, Uusküla A. Post-acute sequelae of COVID-19 among hospitalized patients in Estonia: Nationwide matched cohort study. PLoS One 2022; 17:e0278057. [PMID: 36417409 PMCID: PMC9683565 DOI: 10.1371/journal.pone.0278057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/09/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Post-acute COVID-19 sequelae refers to a variety of health complications involving different organ systems that have been described among individuals after acute phase of illness. Data from unselected population groups with long-time follow up is needed to comprehensively describe the full spectrum of post-acute COVID-19 complications. METHODS In this retrospective nationwide cohort study, we used data obtained from electronic health record database. Our primary cohort were adults hospitalized with confirmed COVID-19 and matched (age, sex, Charlson Comorbidity Index) unaffected controls from general population. Individuals included from February 2020 until March 2021 were followed up for 12 months. We estimated risks of all-cause mortality, readmission and incidence of 16 clinical sequelae after acute COVID-19 phase. Using a frailty Cox model, we compared incidences of outcomes in two cohorts. RESULTS The cohort comprised 3949 patients older than 18 years who were alive 30 days after COVID-19 hospital admission and 15511 controls. Among cases 40.3% developed at least one incident clinical sequelae after the acute phase of SARS-CoV-2 infection, which was two times higher than in general population group. We report substantially higher risk of all-cause mortality (adjusted hazard ratio (aHR) = 2.57 (95%CI 2.23-2.96) and hospital readmission aHR = 1.73 (95%CI 1.58-1.90) among hospitalized COVID-19 patients. We found that the risks for new clinical sequalae were significantly higher in COVID-19 patients than their controls, especially for dementia aHR = 4.50 (95% CI 2.35-8.64), chronic lower respiratory disease aHR = 4.39 (95% CI 3.09-6.22), liver disease aHR 4.20 (95% CI 2.01-8.77) and other (than ischemic) forms of heart diseases aHR = 3.39 (95%CI 2.58-4.44). CONCLUSION Our results provide evidence that the post-acute COVID-19 morbidity within the first year after COVID-19 hospitalization is substantial. Risks of all-cause mortality, hospitalisation and majority of clinical sequelae were significantly higher in hospitalized COVID-19 patients than in general population controls and warrant targeted prevention efforts.
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Affiliation(s)
- Anna Tisler
- Institute of Family Medicine and Public Health, University of Tartu, Tartu, Estonia
- * E-mail:
| | - Oliver Stirrup
- Institute for Global Health, University College London, London, United Kingdom
| | - Heti Pisarev
- Institute of Family Medicine and Public Health, University of Tartu, Tartu, Estonia
| | - Ruth Kalda
- Institute of Family Medicine and Public Health, University of Tartu, Tartu, Estonia
| | - Tatjana Meister
- Institute of Family Medicine and Public Health, University of Tartu, Tartu, Estonia
| | - Kadri Suija
- Institute of Family Medicine and Public Health, University of Tartu, Tartu, Estonia
| | - Raivo Kolde
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Marko Piirsoo
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Anneli Uusküla
- Institute of Family Medicine and Public Health, University of Tartu, Tartu, Estonia
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The Comparison of Mutational Progression in SARS-CoV-2: A Short Updated Overview. JOURNAL OF MOLECULAR PATHOLOGY 2022. [DOI: 10.3390/jmp3040018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The COVID-19 pandemic has impacted the world population adversely, posing a threat to human health. In the past few years, various strains of SARS-CoV-2, each with different mutations in its structure, have impacted human health in negative ways. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations influence the virulence, antibody evasion, and Angiotensin-converting enzyme 2 (ACE2) affinity of the virus. These mutations are essential to understanding how a new strain of SARS-CoV-2 has changed and its possible effects on the human body. This review provides an insight into the spike mutations of SARS-CoV-2 variants. As the current scientific data offer a scattered outlook on the various type of mutations, we aimed to categorize the mutations of Beta (B.1.351), Gamma (P.1), Delta (B.1.612.2), and Omicron (B.1.1.529) systematically according to their location in the subunit 1 (S1) and subunit 2 (S2) domains and summarized their consequences as a result. We also compared the miscellany of mutations that have emerged in all four variants to date. The comparison shows that mutations such as D614G and N501Y have emerged in all four variants of concern and that all four variants have multiple mutations within the N-terminal domain (NTD), as in the case of the Delta variant. Other mutations are scattered in the receptor binding domain (RBD) and subdomain 2 (SD2) of the S1 domain. Mutations in RBD or NTD are often associated with antibody evasion. Few mutations lie in the S2 domain in the Beta, Gamma, and Delta variants. However, in the Omicron variant many mutations occupy the S2 domain, hinting towards a much more evasive virus.
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Tan J, Wu Z, Gan L, Zhong Q, Zhu Y, Li Y, Zhang D. Impact of Vaccination and Control Measures on the Fatality of COVID-19: An Ecological Study. J Epidemiol Glob Health 2022; 12:456-471. [PMID: 36161649 PMCID: PMC9513007 DOI: 10.1007/s44197-022-00064-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 09/07/2022] [Indexed: 12/05/2022] Open
Abstract
Background During the COVID-19 pandemic, reducing the case fatality rate (CFR) becomes an urgent goal. Objective This study explored the effect of vaccination and variants on COVID-19 fatality and provide a basis for the adjustment of control measures. Methods This study collected epidemiological information on COVID-19 from January to October 2021. By setting different lag times, we calculated the adjusted CFR. The Spearman correlation coefficient and beta regression were used to explore factors that may affect COVID-19 fatality. Results Every 1% increase in the percentage of full vaccinations may reduce the 3 weeks lagging CFR by 0.66%. Increasing the restrictions on internal movement from level 0 to 1, restrictions on international travel controls from level 2 to 3, and stay-at-home restrictions from level 0 to 2 were associated with an average reduction in 3 weeks lagging CFR of 0.20%, 0.39%, and 0.36%, respectively. Increasing strictness in canceling public events from level 0 to 1 and 2 may reduce the 3 weeks lagging CFR by 0.49% and 0.37, respectively. Increasing the severity of school and workplace closures from level 1 or level 0 to 3 may increase the 3 weeks lagging CFR of 0.39% and 0.83, respectively. Every 1-point increase in the Global Health Security (GHS) index score may increase the 3 weeks lagging CFR by 0.12%. Conclusion A higher percentage of full vaccinations, higher levels of internal movement restrictions, international travel control restrictions, cancelations of public events, and stay-at-home restrictions are factors that may reduce the adjusted CFR.
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Affiliation(s)
- Jinlin Tan
- Department of Epidemiology, School of Public Health, Sun Yat-Sen University, Guangzhou, 510080 Guangdong China
| | - Zhilong Wu
- Department of Tuberculosis Control, The Fourth People’s Hospital of Foshan City, Foshan, 528000 Guangdong China
| | - Lin Gan
- Department of Epidemiology, School of Public Health, Sun Yat-Sen University, Guangzhou, 510080 Guangdong China
| | - Qianhong Zhong
- Department of Tuberculosis Control, The Fourth People’s Hospital of Foshan City, Foshan, 528000 Guangdong China
| | - Yajuan Zhu
- Department of Epidemiology, School of Public Health, Sun Yat-Sen University, Guangzhou, 510080 Guangdong China
| | - Yufen Li
- Department of Epidemiology, School of Public Health, Sun Yat-Sen University, Guangzhou, 510080 Guangdong China
| | - Dingmei Zhang
- Department of Epidemiology, School of Public Health, Sun Yat-Sen University, Guangzhou, 510080 Guangdong China
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Niu Y, Luo L, Yang S, Abudurusuli G, Wang X, Zhao Z, Rui J, Li Z, Deng B, Liu W, Zhang Z, Li K, Liu C, Li P, Huang J, Yang T, Wang Y, Chen T, Li Q. Comparison of epidemiological characteristics and transmissibility of different strains of COVID-19 based on the incidence data of all local outbreaks in China as of March 1, 2022. Front Public Health 2022; 10:949594. [PMID: 36187650 PMCID: PMC9521362 DOI: 10.3389/fpubh.2022.949594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 08/29/2022] [Indexed: 01/21/2023] Open
Abstract
Background The epidemiological characteristics and transmissibility of Coronavirus Disease 2019 (COVID-19) may undergo changes due to the mutation of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) strains. The purpose of this study is to compare the differences in the outbreaks of the different strains with regards to aspects such as epidemiological characteristics, transmissibility, and difficulties in prevention and control. Methods COVID-19 data from outbreaks of pre-Delta strains, the Delta variant and Omicron variant, were obtained from the Chinese Center for Disease Control and Prevention (CDC). Case data were collected from China's direct-reporting system, and the data concerning outbreaks were collected by on-site epidemiological investigators and collated by the authors of this paper. Indicators such as the effective reproduction number (R eff), time-dependent reproduction number (R t), rate of decrease in transmissibility (RDT), and duration from the illness onset date to the diagnosed date (D ID )/reported date (D IR ) were used to compare differences in transmissibility between pre-Delta strains, Delta variants and Omicron variants. Non-parametric tests (namely the Kruskal-Wallis H and Mean-Whitney U tests) were used to compare differences in epidemiological characteristics and transmissibility between outbreaks of different strains. P < 0.05 indicated that the difference was statistically significant. Results Mainland China has maintained a "dynamic zero-out strategy" since the first case was reported, and clusters of outbreaks have occurred intermittently. The strains causing outbreaks in mainland China have gone through three stages: the outbreak of pre-Delta strains, the outbreak of the Delta variant, and outbreaks involving the superposition of Delta and Omicron variant strains. Each outbreak of pre-Delta strains went through two stages: a rising stage and a falling stage, Each outbreak of the Delta variant and Omicron variant went through three stages: a rising stage, a platform stage and a falling stage. The maximum R eff value of Omicron variant outbreaks was highest (median: 6.7; ranged from 5.3 to 8.0) and the differences were statistically significant. The RDT value of outbreaks involving pre-Delta strains was smallest (median: 91.4%; [IQR]: 87.30-94.27%), and the differences were statistically significant. The D ID and D IR for all strains was mostly in a range of 0-2 days, with more than 75%. The range of duration for outbreaks of pre-Delta strains was the largest (median: 20 days, ranging from 1 to 61 days), and the differences were statistically significant. Conclusion With the evolution of the virus, the transmissibility of the variants has increased. The transmissibility of the Omicron variant is higher than that of both the pre-Delta strains and the Delta variant, and is more difficult to suppress. These findings provide us with get a more clear and precise picture of the transmissibility of the different variants in the real world, in accordance with the findings of previous studies. R eff is more suitable than R t for assessing the transmissibility of the disease during an epidemic outbreak.
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Affiliation(s)
- Yan Niu
- Public Health Emergency Center, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Li Luo
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Shiting Yang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Guzainuer Abudurusuli
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Xiaoye Wang
- Public Health Emergency Center, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zeyu Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Jia Rui
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Zhuoyang Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Bin Deng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Weikang Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Zhe Zhang
- School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Kangguo Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Chan Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Peihua Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Jiefeng Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Tianlong Yang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Yao Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Tianmu Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China,Tianmu Chen
| | - Qun Li
- Public Health Emergency Center, Chinese Center for Disease Control and Prevention, Beijing, China,*Correspondence: Qun Li
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Clinical and genomic signatures of SARS-CoV-2 Delta breakthrough infections in New York. EBioMedicine 2022; 82:104141. [PMID: 35906172 PMCID: PMC9323230 DOI: 10.1016/j.ebiom.2022.104141] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 12/20/2022] Open
Abstract
Background In 2021, Delta became the predominant SARS-CoV-2 variant worldwide. While vaccines have effectively prevented COVID-19 hospitalization and death, vaccine breakthrough infections increasingly occurred. The precise role of clinical and genomic determinants in Delta infections is not known, and whether they contributed to increased rates of breakthrough infections compared to unvaccinated controls. Methods We studied SARS-CoV-2 variant distribution, dynamics, and adaptive selection over time in relation to vaccine status, phylogenetic relatedness of viruses, full genome mutation profiles, and associated clinical and demographic parameters. Findings We show a steep and near-complete replacement of circulating variants with Delta between May and August 2021 in metropolitan New York. We observed an increase of the Delta sublineage AY.25 (14% in vaccinated, 7% in unvaccinated), its spike mutation S112L, and AY.44 (8% in vaccinated, 2% in unvaccinated) with its nsp12 mutation F192V in breakthroughs. Delta infections were associated with younger age and lower hospitalization rates than Alpha. Delta breakthrough infections increased significantly with time since vaccination, and, after adjusting for confounders, they rose at similar rates as in unvaccinated individuals. Interpretation We observed a modest adaptation of Delta genomes in breakthrough infections in New York, suggesting an improved genomic framework to support Delta's epidemic growth in times of waning vaccine protection despite limited impact on vaccine escape. Funding The study was supported by NYU institutional funds. The NYULH Genome Technology Center is partially supported by the Cancer Center Support Grant P30CA016087 at the Laura and Isaac Perlmutter Cancer Center.
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Shrestha L, Lin MJ, Xie H, Mills MG, Mohamed Bakhash SA, Gaur VP, Livingston RJ, Castor J, Bruce EA, Botten JW, Huang ML, Jerome KR, Greninger AL, Roychoudhury P. Clinical performance characteristics of the Swift Normalase Amplicon Panel for sensitive recovery of SARS-CoV-2 genomes. J Mol Diagn 2022; 24:963-976. [PMID: 35863699 PMCID: PMC9290336 DOI: 10.1016/j.jmoldx.2022.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 03/24/2022] [Accepted: 05/27/2022] [Indexed: 11/18/2022] Open
Abstract
Amplicon-based sequencing methods are central in characterizing the diversity, transmission, and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but need to be rigorously assessed for clinical utility. Herein, we validated the Swift Biosciences' SARS-CoV-2 Swift Normalase Amplicon Panels using remnant clinical specimens. High-quality genomes meeting our established library and sequence quality criteria were recovered from positive specimens, with 95% limit of detection of 40.08 SARS-CoV-2 copies/PCR. Breadth of genome recovery was evaluated across a range of CT values (11.3 to 36.7; median, 21.6). Of 428 positive samples, 413 (96.5%) generated genomes with <10% unknown bases, with a mean genome coverage of 13,545× ± SD 8382×. No genomes were recovered from PCR-negative specimens (n = 30) or from specimens positive for non–SARS-CoV-2 respiratory viruses (n = 20). Compared with whole-genome shotgun metagenomic sequencing (n = 14) or Sanger sequencing for the spike gene (n = 11), pairwise identity between consensus sequences was 100% in all cases, with highly concordant allele frequencies (R2 = 0.99) between Swift and shotgun libraries. When samples from different clades were mixed at varying ratios, expected variants were detected even in 1:99 mixtures. When deployed as a clinical test, 268 tests were performed in the first 23 weeks, with a median turnaround time of 11 days, ordered primarily for outbreak investigations and infection control.
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Affiliation(s)
- Lasata Shrestha
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Michelle J Lin
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Margaret G Mills
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | | | - Vinod P Gaur
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Robert J Livingston
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Jared Castor
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Emily A Bruce
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT
| | - Jason W Botten
- Department of Medicine, University of Vermont, Burlington, VT
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Keith R Jerome
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA.
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA.
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Zisis SN, Durieux JC, Mouchati C, Perez JA, McComsey GA. The Protective Effect of Coronavirus Disease 2019 (COVID-19) Vaccination on Postacute Sequelae of COVID-19: A Multicenter Study From a Large National Health Research Network. Open Forum Infect Dis 2022; 9:ofac228. [PMID: 35818362 PMCID: PMC9129153 DOI: 10.1093/ofid/ofac228] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/05/2022] [Indexed: 11/19/2022] Open
Abstract
Background Coronavirus disease 2019 (COVID-19) vaccines have been proven to decrease the severity of acute-phase infection; however, little is known about their effect on postacute sequelae of COVID-19 (PASC). Methods Patients with confirmed COVID-19 diagnosis and minimum age of 18 years with 3-month follow-up postdiagnosis between 21 September 2020 and 14 December 2021 were identified from the TriNetX Research Network platform. The primary outcomes consisted of new-onset or persistent symptoms, new-onset diagnoses, and death and were compared between vaccine and no-vaccine groups. Results At baseline, 1 578 719 patients with confirmed COVID-19 were identified and 1.6% (n = 25 225) completed vaccination. After matching, there were no differences (P > .05) in demographics or preexisting comorbidities. At 28 days following COVID-19 diagnosis, the incidence of hypertension was 13.52 per 1000, diabetes was 5.98 per 1000, thyroid disease was 3.80 per 1000, heart disease was 15.41 per 1000, and mental disorders was 14.77 per 1000 in the vaccine cohort. At 90 days following COVID-19 diagnosis, the relative risk of hypertension was 0.33 (95% confidence interval [CI], .26-.42), diabetes was 0.28 (95% CI, .20-.38), heart disease was 0.35 (95% CI, .29-.44), and death was 0.21 (95% CI, .16-.27). Differences in both 28- and 90-day risk between the vaccine and no-vaccine cohorts were observed for each outcome, and there was enough evidence (P < .05) to suggest that these differences were attributed to the vaccine. Conclusions Our data suggest that COVID-19 vaccine is protective against PASC symptoms, new onset of health conditions, and mortality.
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Affiliation(s)
- Sokratis N Zisis
- School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jared C Durieux
- Clinical Research Center, University Hospitals Health System, Cleveland, Ohio, USA
| | - Christian Mouchati
- School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jamie A Perez
- Clinical Research Center, University Hospitals Health System, Cleveland, Ohio, USA
| | - Grace A McComsey
- School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Clinical Research Center, University Hospitals Health System, Cleveland, Ohio, USA
- Department of Pediatrics and Medicine, Case Western Reserve University, Cleveland, Ohio, USA
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Sequencing during Times of Change: Evaluating SARS-CoV-2 Clinical Samples during the Transition from the Delta to Omicron Wave. Viruses 2022; 14:v14071408. [PMID: 35891388 PMCID: PMC9320617 DOI: 10.3390/v14071408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/21/2022] [Accepted: 06/24/2022] [Indexed: 11/18/2022] Open
Abstract
The pandemic of SARS-CoV-2 is characterized by the emergence of new variants of concern (VOCs) that supplant previous waves of infection. Here, we describe our investigation of the lineages and host-specific mutations identified in a particularly vulnerable population of predominantly older and immunosuppressed SARS-CoV-2-infected patients seen at our medical center in Chicago during the transition from the Delta to Omicron wave. We compare two primer schemes, ArticV4.1 and VarSkip2, used for short read amplicon sequencing, and describe our strategy for bioinformatics analysis that facilitates identifying lineage-associated mutations and host-specific mutations that arise during infection. This study illustrates the ongoing evolution of SARS-CoV-2 VOCs in our community and documents novel constellations of mutations that arise in individual patients. The ongoing evaluation of the evolution of SARS-CoV-2 during this pandemic is important for informing our public health strategies.
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11
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Chia PY, Ong SWX, Chiew CJ, Ang LW, Chavatte JM, Mak TM, Cui L, Kalimuddin S, Chia WN, Tan CW, Chai LYA, Tan SY, Zheng S, Lin RTP, Wang L, Leo YS, Lee VJ, Lye DC, Young BE. Virological and serological kinetics of SARS-CoV-2 Delta variant vaccine breakthrough infections: a multicentre cohort study. Clin Microbiol Infect 2022; 28:612.e1-612.e7. [PMID: 34826623 DOI: 10.1101/2021.1107.1128.21261295v21261291] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 10/16/2021] [Accepted: 11/06/2021] [Indexed: 05/23/2023]
Abstract
OBJECTIVES Highly effective vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been developed but variants of concerns are worrisome, especially B.1.617.2 (Delta) which has rapidly spread across the world. We aim to study if vaccination alters virological and serological kinetics in breakthrough infections. METHODS We conducted a multicentre retrospective cohort study of patients in Singapore who had received a licensed mRNA vaccine and been admitted to hospital with B.1.617.2 SARS-CoV-2 infection. We compared clinical features, virological and serological kinetics (anti-nucleocapsid, anti-spike and surrogate virus neutralization titres) between fully vaccinated and unvaccinated individuals. RESULTS Out of 218 individuals with B.1.617.2 infection, 84 received an mRNA vaccine of which 71 were fully vaccinated, 130 were unvaccinated and four received a non-mRNA vaccine. Despite significantly older age in the vaccine breakthrough group, only 2.8% (2/71) developed severe COVID-19 requiring oxygen supplementation compared with 53.1% (69/130) in the unvaccinated group (p < 0.001). Odds of severe COVID-19 following vaccination were significantly lower (adjusted odds ratio 0.07 95% CI 0.015-0.335, p 0.001). PCR cycle threshold values were similar between vaccinated and unvaccinated groups at diagnosis, but viral loads decreased faster in vaccinated individuals. Early, robust boosting of anti-spike protein antibodies was observed in vaccinated patients; however, these titres were significantly lower against B.1.617.2 than the wildtype vaccine strain. DISCUSSION The mRNA vaccines are highly effective at preventing symptomatic and severe COVID-19 associated with B.1.617.2 infection. Vaccination is associated with faster decline in viral RNA load and a robust serological response. Vaccination remains a key strategy for control of the COVID-19 pandemic.
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Affiliation(s)
- Po Ying Chia
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Sean Wei Xiang Ong
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore
| | - Calvin J Chiew
- National Centre for Infectious Diseases, Singapore; Ministry of Health, Singapore
| | - Li Wei Ang
- National Centre for Infectious Diseases, Singapore
| | | | - Tze-Minn Mak
- National Centre for Infectious Diseases, Singapore
| | - Lin Cui
- National Centre for Infectious Diseases, Singapore
| | - Shirin Kalimuddin
- Singapore General Hospital, Singapore; Duke-NUS Medical School, National University of Singapore, Singapore
| | - Wan Ni Chia
- Duke-NUS Medical School, National University of Singapore, Singapore
| | - Chee Wah Tan
- Duke-NUS Medical School, National University of Singapore, Singapore
| | - Louis Yi Ann Chai
- National University Health System, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | | | | | - Linfa Wang
- Duke-NUS Medical School, National University of Singapore, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - David Chien Lye
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Barnaby Edward Young
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.
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12
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Chia PY, Ong SWX, Chiew CJ, Ang LW, Chavatte JM, Mak TM, Cui L, Kalimuddin S, Chia WN, Tan CW, Chai LYA, Tan SY, Zheng S, Lin RTP, Wang L, Leo YS, Lee VJ, Lye DC, Young BE. Virological and serological kinetics of SARS-CoV-2 Delta variant vaccine breakthrough infections: a multicentre cohort study. Clin Microbiol Infect 2022. [PMID: 34826623 DOI: 10.1101/2021.07.28.21261295] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
OBJECTIVES Highly effective vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been developed but variants of concerns are worrisome, especially B.1.617.2 (Delta) which has rapidly spread across the world. We aim to study if vaccination alters virological and serological kinetics in breakthrough infections. METHODS We conducted a multicentre retrospective cohort study of patients in Singapore who had received a licensed mRNA vaccine and been admitted to hospital with B.1.617.2 SARS-CoV-2 infection. We compared clinical features, virological and serological kinetics (anti-nucleocapsid, anti-spike and surrogate virus neutralization titres) between fully vaccinated and unvaccinated individuals. RESULTS Out of 218 individuals with B.1.617.2 infection, 84 received an mRNA vaccine of which 71 were fully vaccinated, 130 were unvaccinated and four received a non-mRNA vaccine. Despite significantly older age in the vaccine breakthrough group, only 2.8% (2/71) developed severe COVID-19 requiring oxygen supplementation compared with 53.1% (69/130) in the unvaccinated group (p < 0.001). Odds of severe COVID-19 following vaccination were significantly lower (adjusted odds ratio 0.07 95% CI 0.015-0.335, p 0.001). PCR cycle threshold values were similar between vaccinated and unvaccinated groups at diagnosis, but viral loads decreased faster in vaccinated individuals. Early, robust boosting of anti-spike protein antibodies was observed in vaccinated patients; however, these titres were significantly lower against B.1.617.2 than the wildtype vaccine strain. DISCUSSION The mRNA vaccines are highly effective at preventing symptomatic and severe COVID-19 associated with B.1.617.2 infection. Vaccination is associated with faster decline in viral RNA load and a robust serological response. Vaccination remains a key strategy for control of the COVID-19 pandemic.
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Affiliation(s)
- Po Ying Chia
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Sean Wei Xiang Ong
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore
| | - Calvin J Chiew
- National Centre for Infectious Diseases, Singapore; Ministry of Health, Singapore
| | - Li Wei Ang
- National Centre for Infectious Diseases, Singapore
| | | | - Tze-Minn Mak
- National Centre for Infectious Diseases, Singapore
| | - Lin Cui
- National Centre for Infectious Diseases, Singapore
| | - Shirin Kalimuddin
- Singapore General Hospital, Singapore; Duke-NUS Medical School, National University of Singapore, Singapore
| | - Wan Ni Chia
- Duke-NUS Medical School, National University of Singapore, Singapore
| | - Chee Wah Tan
- Duke-NUS Medical School, National University of Singapore, Singapore
| | - Louis Yi Ann Chai
- National University Health System, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | | | | | - Linfa Wang
- Duke-NUS Medical School, National University of Singapore, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - David Chien Lye
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Barnaby Edward Young
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.
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13
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Chia PY, Ong SWX, Chiew CJ, Ang LW, Chavatte JM, Mak TM, Cui L, Kalimuddin S, Chia WN, Tan CW, Chai LYA, Tan SY, Zheng S, Lin RTP, Wang L, Leo YS, Lee VJ, Lye DC, Young BE. Virological and serological kinetics of SARS-CoV-2 Delta variant vaccine breakthrough infections: a multicentre cohort study. Clin Microbiol Infect 2022; 28:612.e1-612.e7. [PMID: 34826623 PMCID: PMC8608661 DOI: 10.1016/j.cmi.2021.11.010] [Citation(s) in RCA: 145] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 10/16/2021] [Accepted: 11/06/2021] [Indexed: 12/16/2022]
Abstract
OBJECTIVES Highly effective vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been developed but variants of concerns are worrisome, especially B.1.617.2 (Delta) which has rapidly spread across the world. We aim to study if vaccination alters virological and serological kinetics in breakthrough infections. METHODS We conducted a multicentre retrospective cohort study of patients in Singapore who had received a licensed mRNA vaccine and been admitted to hospital with B.1.617.2 SARS-CoV-2 infection. We compared clinical features, virological and serological kinetics (anti-nucleocapsid, anti-spike and surrogate virus neutralization titres) between fully vaccinated and unvaccinated individuals. RESULTS Out of 218 individuals with B.1.617.2 infection, 84 received an mRNA vaccine of which 71 were fully vaccinated, 130 were unvaccinated and four received a non-mRNA vaccine. Despite significantly older age in the vaccine breakthrough group, only 2.8% (2/71) developed severe COVID-19 requiring oxygen supplementation compared with 53.1% (69/130) in the unvaccinated group (p < 0.001). Odds of severe COVID-19 following vaccination were significantly lower (adjusted odds ratio 0.07 95% CI 0.015-0.335, p 0.001). PCR cycle threshold values were similar between vaccinated and unvaccinated groups at diagnosis, but viral loads decreased faster in vaccinated individuals. Early, robust boosting of anti-spike protein antibodies was observed in vaccinated patients; however, these titres were significantly lower against B.1.617.2 than the wildtype vaccine strain. DISCUSSION The mRNA vaccines are highly effective at preventing symptomatic and severe COVID-19 associated with B.1.617.2 infection. Vaccination is associated with faster decline in viral RNA load and a robust serological response. Vaccination remains a key strategy for control of the COVID-19 pandemic.
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Affiliation(s)
- Po Ying Chia
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Sean Wei Xiang Ong
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore
| | - Calvin J Chiew
- National Centre for Infectious Diseases, Singapore; Ministry of Health, Singapore
| | - Li Wei Ang
- National Centre for Infectious Diseases, Singapore
| | | | - Tze-Minn Mak
- National Centre for Infectious Diseases, Singapore
| | - Lin Cui
- National Centre for Infectious Diseases, Singapore
| | - Shirin Kalimuddin
- Singapore General Hospital, Singapore; Duke-NUS Medical School, National University of Singapore, Singapore
| | - Wan Ni Chia
- Duke-NUS Medical School, National University of Singapore, Singapore
| | - Chee Wah Tan
- Duke-NUS Medical School, National University of Singapore, Singapore
| | - Louis Yi Ann Chai
- National University Health System, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | | | | | - Linfa Wang
- Duke-NUS Medical School, National University of Singapore, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - David Chien Lye
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Barnaby Edward Young
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.
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14
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Gallais F, Gantner P, Planas D, Solis M, Bruel T, Pierre F, Soulier E, Rossolillo P, Fourati S, Sibilia J, Schwartz O, Fafi-Kremer S. Case Report: Evolution of Humoral and Cellular Immunity in Two COVID-19 Breakthrough Infections After BNT162b2 Vaccine. Front Immunol 2022; 13:790212. [PMID: 35281046 PMCID: PMC8905643 DOI: 10.3389/fimmu.2022.790212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/31/2022] [Indexed: 11/21/2022] Open
Abstract
Background SARS-CoV-2 breakthrough infections after complete vaccination are increasing whereas their determinants remain uncharacterized. Methods We analyzed two cases of post-vaccination SARS-CoV-2 infections by α and β variants, respectively. For each participant both humoral (binding and neutralizing antibodies) and cellular (activation markers and cytokine expression) immune responses were characterized longitudinally. Results The first participant (P1) was infected by an α variant and displayed an extended and short period of viral excretion and symptom. Analysis of cellular and humoral response 72 h post-symptom onset revealed that P1 failed at developing neutralizing antibodies and a potent CD4 memory response (lack of SARS-CoV-2 specific CD4+IL-2+ cells) and CD8 effector response (CD8+IFNγ+ cells). The second participant (P2) developed post-vaccination SARS-CoV-2 infection by a β variant, associated with a short period of viral excretion and symptoms. Despite displaying initially high levels and polyfunctional T cell responses, P2 lacked initial β-directed neutralizing antibodies. Both participants developed and/or increased their neutralization activity and cellular responses against all variants, namely, β and δ variants that lasts up to 3 months after breakthrough infection. Conclusions An analysis of cellular and humoral response suggests two possible mechanisms of breakthrough infection: a poor immune response to vaccine and viral evasion to neutralizing antibodies.
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Affiliation(s)
- Floriane Gallais
- CHU de Strasbourg, Laboratoire de Virologie, Strasbourg, France.,Strasbourg University, Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche Scientifique Immuno-Rhumathologie Moléculaire (IRM UMR-S) 1109, Strasbourg, France
| | - Pierre Gantner
- CHU de Strasbourg, Laboratoire de Virologie, Strasbourg, France.,Strasbourg University, Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche Scientifique Immuno-Rhumathologie Moléculaire (IRM UMR-S) 1109, Strasbourg, France
| | - Delphine Planas
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 3569, Paris, France.,Vaccine Research Institute, Creteil, France
| | - Morgane Solis
- CHU de Strasbourg, Laboratoire de Virologie, Strasbourg, France.,Strasbourg University, Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche Scientifique Immuno-Rhumathologie Moléculaire (IRM UMR-S) 1109, Strasbourg, France
| | - Timothée Bruel
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 3569, Paris, France.,Vaccine Research Institute, Creteil, France
| | - Florian Pierre
- CHU de Strasbourg, Laboratoire de Virologie, Strasbourg, France.,Strasbourg University, Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche Scientifique Immuno-Rhumathologie Moléculaire (IRM UMR-S) 1109, Strasbourg, France
| | - Eric Soulier
- CHU de Strasbourg, Laboratoire de Virologie, Strasbourg, France.,Strasbourg University, Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche Scientifique Immuno-Rhumathologie Moléculaire (IRM UMR-S) 1109, Strasbourg, France
| | - Paola Rossolillo
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, Unité Mixte de Recherche (UMR) 7104, Institut National de la Santé et de la Recherche Médicale, Université de Strasbourg, Illkirch, France
| | - Slim Fourati
- Department of Virology, Hôpital Henri Mondor, Créteil, France.,Mondor Institute for Biomedical Research (IIMRB), Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 955, Créteil, France
| | - Jean Sibilia
- CHU de Strasbourg, Département de Rhumathologie, Strasbourg, France
| | - Olivier Schwartz
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 3569, Paris, France.,Vaccine Research Institute, Creteil, France
| | - Samira Fafi-Kremer
- CHU de Strasbourg, Laboratoire de Virologie, Strasbourg, France.,Strasbourg University, Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche Scientifique Immuno-Rhumathologie Moléculaire (IRM UMR-S) 1109, Strasbourg, France
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15
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Tian D, Song Y, Zhang M, Pan Y, Ge Z, Zhang Y, Ren X, Wen J, Xu Y, Guo H, Yang P, Chen Z, Xu W. Genomic, immunological and clinical analysis of COVID-19 vaccine breakthrough infections in Beijing, China. J Med Virol 2022; 94:2237-2249. [PMID: 35112366 PMCID: PMC9015436 DOI: 10.1002/jmv.27636] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 11/07/2022]
Abstract
As the COVID-19 pandemic is still ongoing and SARS-CoV-2 variants are circulating worldwide, an increasing number of breakthrough infections are being detected despite the good efficacy of COVID-19 vaccines. Data on 88 COVID-19 breakthrough cases (breakthrough infections group) and 41 unvaccinated cases (unvaccinated group) from 1 June to 22 August, 2021, were extracted from a cloud database established at Beijing Ditan Hospital to evaluate the clinical, immunological and genomic characteristics of COVID-19 breakthrough infections. Among these 129 COVID-19 cases, 33 whole genomes were successfully sequenced, of which 23 were Delta variants, including 15 from the breakthrough infections group. Asymptomatic and mild cases predominated in both groups, but 2 patients developed severe disease in the unvaccinated group. The median time of viral shedding in the breakthrough infections group was significantly lower than that in the unvaccinated group (P = 0.003). In the breakthrough infections group, the IgG titres showed a significantly increasing trend (P =0.007), and the CD4+ T lymphocyte count was significantly elevated (P=0.018). For people infected with the Delta variant in the two groups, no significant difference was observed in either the RT-qPCR results or viral shedding time. In conclusion, among vaccinated patients, the cases of COVID-19 vaccine breakthrough infections were mainly asymptomatic and mild, IgG titres were significantly increased and rose rapidly, and the viral shedding time was shorter. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Di Tian
- Emergency Department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Yang Song
- National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Man Zhang
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Yang Pan
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Ziruo Ge
- Emergency Department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Yao Zhang
- Emergency Department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Xingxiang Ren
- Emergency Department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Jing Wen
- Emergency Department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Yanli Xu
- Emergency Department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Hong Guo
- National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Peng Yang
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Zhihai Chen
- Emergency Department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Wenbo Xu
- National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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16
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Yang WT, Huang WH, Liao TL, Hsiao TH, Chuang HN, Liu PY. SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Infect Drug Resist 2022; 15:373-385. [PMID: 35140483 PMCID: PMC8820839 DOI: 10.2147/idr.s344099] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/06/2022] [Indexed: 12/12/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread rapidly over the world and claimed million lives. The virus evolves constantly, and a swarm of mutants is a now major concern globally. Distinct variants could have independently converged on same mutation, despite being detected in different geographic regions, which suggested it could confer an evolutionary advantage. E484K has rapidly emerged and has frequently been detected in several SARS-CoV-2 variants of concern. In this study, we review the epidemiology and impact of E484K, its effects on neutralizing effect of several monoclonal antibodies, convalescent plasma, and post-vaccine sera.
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Affiliation(s)
- Wan-Ting Yang
- Division of Infection, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Wei-Hsuan Huang
- Division of Infection, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Tsai-Ling Liao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Tzu-Hung Hsiao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Han-Ni Chuang
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Po-Yu Liu
- Division of Infection, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
- Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan
- Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan
- Correspondence: Po-Yu Liu, Division of Infection, Department of Internal Medicine, Taichung Veterans General Hospital, 1650 Taiwan Boulevard Sect. 4, Taichung, 4070, Taiwan, Tel +886 4-23592525, Fax +886 4-2359-5046, Email
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17
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Bruxvoort KJ, Sy LS, Qian L, Ackerson BK, Luo Y, Lee GS, Tian Y, Florea A, Takhar HS, Tubert JE, Talarico CA, Tseng HF. Real-world effectiveness of the mRNA-1273 vaccine against COVID-19: Interim results from a prospective observational cohort study. LANCET REGIONAL HEALTH. AMERICAS 2022; 6:100134. [PMID: 34849505 PMCID: PMC8614600 DOI: 10.1016/j.lana.2021.100134] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Background Phase 3 trials found mRNA-1273 was highly effective in preventing COVID-19. We conducted a prospective cohort study at Kaiser Permanente Southern California (KPSC) to determine the real-world vaccine effectiveness (VE) of mRNA-1273 in preventing COVID-19 infection and severe disease. Methods For this planned interim analysis, individuals aged ≥18 years receiving 2 doses of mRNA-1273 ≥24 days apart (18/12/2020-31/03/2021) were 1:1 matched to randomly selected unvaccinated individuals by age, sex, and race/ethnicity, with follow-up through 30/06/2021. Outcomes were COVID-19 infection (SARS-CoV-2 positive molecular test or COVID-19 diagnosis code) or severe disease (COVID-19 hospitalization and COVID-19 hospital death). Adjusted hazard ratios (aHR) and confidence intervals (CI) for COVID-19 outcomes comparing vaccinated and unvaccinated individuals were estimated by Cox proportional hazards models accounting for multiple comparisons. Adjusted VE was calculated as (1-aHR)x100. Whole genome sequencing was performed on SARS-CoV-2 positive specimens from the KPSC population. Findings This analysis included 352,878 recipients of 2 doses of mRNA-1273 matched to 352,878 unvaccinated individuals. VE (99·3% CI) against COVID-19 infection was 87·4% (84·8–89·6%). VE against COVID-19 hospitalization and hospital death was 95·8% (90·7–98·1%) and 97·9% (66·9-99·9%), respectively. VE was higher against symptomatic (88·3% [98·3% CI: 86·1–90·2%]) than asymptomatic COVID-19 (72·7% [53·4–84·0%]), but was generally similar across age, sex, and racial/ethnic subgroups. VE among individuals with history of COVID-19 ranged from 8·2–33·6%. The most prevalent variants were Alpha (41·6%), Epsilon (17·5%), Delta (11·5%), and Gamma (9·1%), with Delta increasing to 54·0% of variants by June 2021. Interpretation These interim results provide reassuring evidence of the VE of 2 doses of mRNA-1273 across age, sex, and racial/ethnic subgroups, and against asymptomatic and symptomatic COVID-19, and severe COVID-19 outcomes. Among individuals with history of COVID-19, mRNA-1273 vaccination may offer added protection beyond immunity acquired from prior infection. Longer follow-up is needed to fully evaluate VE of mRNA-1273 against emerging SARS-CoV-2 variants. Funding Moderna Inc.
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Affiliation(s)
- Katia J Bruxvoort
- Kaiser Permanente Southern California, Pasadena, CA, USA.,University of Alabama at Birmingham, Birmingham, AL, USA
| | - Lina S Sy
- Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Lei Qian
- Kaiser Permanente Southern California, Pasadena, CA, USA
| | | | - Yi Luo
- Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Gina S Lee
- Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Yun Tian
- Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Ana Florea
- Kaiser Permanente Southern California, Pasadena, CA, USA
| | | | - Julia E Tubert
- Kaiser Permanente Southern California, Pasadena, CA, USA
| | | | - Hung Fu Tseng
- Kaiser Permanente Southern California, Pasadena, CA, USA.,Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA, USA
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18
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Prevalence of SARS-CoV-2 Variants of Concern and Variants of Interest in COVID-19 Breakthrough Infections in a Hospital in Monterrey, Mexico. Viruses 2022; 14:v14010154. [PMID: 35062359 PMCID: PMC8781434 DOI: 10.3390/v14010154] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/06/2022] [Accepted: 01/11/2022] [Indexed: 02/06/2023] Open
Abstract
SARS-CoV-2 variants of concern (VOCs) or of interest (VOIs) causing vaccine breakthrough infections pose an increased risk to worldwide public health. An observational case-control study was performed of SARS-CoV-2 vaccine breakthrough infections in hospitalized or ambulatory patients in Monterrey, Mexico, from April through August 2021. Vaccination breakthrough was defined as a SARS-CoV-2 infection that occurred any time after 7 days of inoculation with partial (e.g., first dose of two-dose vaccines) or complete immunization (e.g., second dose of two-dose vaccines or single-dose vaccine, accordingly). Case group patients (n = 53) had partial or complete vaccination schemes with CanSino (45%), Sinovac (19%), Pfizer/BioNTech (15%), and AstraZeneca/Oxford (15%). CanSino was administered most frequently in ambulatory patients (p < 0.01). The control group (n = 19) received no COVID-19 vaccines. Among SARS-CoV-2 variants detected by whole-genome sequencing, VOC Delta B.1.617.2 predominated in vaccinated ambulatory patients (p < 0.01) and AY.4 in hospitalized patients (p = 0.04); VOI Mu B.1.621 was detected in four (7.55%) vaccinated patients. SARS-CoV-2 breakthrough infections in our hospital occurred mostly in patients vaccinated with CanSino due to the higher prevalence of CanSino vaccine administration in our population. These patients developed mild COVID-19 symptoms not requiring hospitalization. The significance of this study lies on the detection of SARS-CoV-2 variants compromising the efficacy of local immunization therapies in Monterrey, Mexico.
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19
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Zhang M, Liang Y, Yu D, Du B, Cheng W, Li L, Yu Z, Luo S, Zhang Y, Wang H, Zhang X, Zhang W. A systematic review of Vaccine Breakthrough Infections by SARS-CoV-2 Delta Variant. Int J Biol Sci 2022; 18:889-900. [PMID: 35002532 PMCID: PMC8741840 DOI: 10.7150/ijbs.68973] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/02/2021] [Indexed: 12/11/2022] Open
Abstract
Vaccines are proving to be highly effective in controlling hospitalization and deaths associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, as shown by clinical trials and real-world evidence. However, a deadly second wave of coronavirus disease 2019 (COVID-19), infected by SARS-CoV-2 variants, especially the Delta (B.1.617.2) variant, with an increased number of post-vaccination breakthrough infections were reported in the world recently. Actually, Delta variant not only resulted in a severe surge of vaccine breakthrough infections which was accompanied with high viral load and transmissibility, but also challenged the development of effective vaccines. Therefore, the biological characteristics and epidemiological profile of Delta variant, the current status of Delta variant vaccine breakthrough infections and the mechanism of vaccine breakthrough infections were discussed in this article. In addition, the significant role of the Delta variant spike (S) protein in the mechanism of immune escape of SARS-CoV-2 was highlighted in this article. In particular, we further discussed key points on the future SARS-CoV-2 vaccine research and development, hoping to make a contribution to the early, accurate and rapid control of the COVID-19 epidemic.
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Affiliation(s)
- Mengxin Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Ying Liang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Dongsheng Yu
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, China
| | - Bang Du
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Weyland Cheng
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Lifeng Li
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Zhidan Yu
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Shuying Luo
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Yaodong Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Huanmin Wang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Xianwei Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Wancun Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
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20
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Servellita V, Morris MK, Sotomayor-Gonzalez A, Gliwa AS, Torres E, Brazer N, Zhou A, Hernandez KT, Sankaran M, Wang B, Wong D, Wang C, Zhang Y, Reyes KR, Glasner D, Deng X, Streithorst J, Miller S, Frias E, Rodgers M, Cloherty G, Hackett J, Hanson C, Wadford D, Philip S, Topper S, Sachdev D, Chiu CY. Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California. Nat Microbiol 2022; 7:277-288. [PMID: 35013591 DOI: 10.1038/s41564-021-01041-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/02/2021] [Indexed: 01/19/2023]
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.
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Affiliation(s)
- Venice Servellita
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Mary Kate Morris
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Amelia S Gliwa
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | | | - Noah Brazer
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | | | | | | | - Baolin Wang
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Daniel Wong
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Candace Wang
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Yueyuan Zhang
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Kevin R Reyes
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Dustin Glasner
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Xianding Deng
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Jessica Streithorst
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | | | | | | | | | - Carl Hanson
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Debra Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Susan Philip
- San Francisco Department of Public Health, San Francisco, CA, USA
| | | | - Darpun Sachdev
- San Francisco Department of Public Health, San Francisco, CA, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. .,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA. .,Department of Medicine, University of California San Francisco, San Francisco, CA, USA. .,Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA.
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21
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Rümke LW, Groenveld FC, van Os YMG, Praest P, Tanja AAN, de Jong DTCM, Symons J, Schuurman R, Reinders T, Hofstra LM, Nierkens S, Thijsen SFT, Heron M, Lebbink RJ, Beekman JM, Nijhuis M, Wensing AMJ. In-depth Characterization of Vaccine Breakthrough Infections With SARS-CoV-2 Among Health Care Workers in a Dutch Academic Medical Center. Open Forum Infect Dis 2022; 9:ofab553. [PMID: 34988250 PMCID: PMC8714358 DOI: 10.1093/ofid/ofab553] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/03/2021] [Indexed: 11/12/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 infection after coronavirus disease 2019 vaccination raises concerns about the emergence of vaccine escape variants. Here we characterize 14 breakthrough infections among 5860 fully vaccinated Dutch health care workers ≥14 days after the final dose of vaccination with either BNT162b2, mRNA-1273, or Ad26.COV2.S. These breakthrough infections presented with regular B.1.1.7 (Alpha) and B.1.617.2 (Delta) variants and high viral loads, despite normal vaccine-induced B- and T-cell immune responses detected by live virus neutralization assays and ELISpot. High-risk exposure settings, such as in households, indicate a potential risk of viral transmission despite full vaccination.
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Affiliation(s)
- Lidewij W Rümke
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Femke C Groenveld
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Yvonne M G van Os
- Occupational Health Office, Department of Human Resources, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Patrique Praest
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Anniek A N Tanja
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Dorien T C M de Jong
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jori Symons
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rob Schuurman
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Tessa Reinders
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - L Marije Hofstra
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Stefan Nierkens
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Steven F T Thijsen
- Department of Medical Microbiology & Immunology, Utrecht, the Netherlands
| | - Michiel Heron
- Department of Medical Microbiology & Immunology, Utrecht, the Netherlands
| | - Robert-Jan Lebbink
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jeffrey M Beekman
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, the Netherlands.,Regenerative Medicine Center Utrecht, University Medical Center, Utrecht University, Utrecht, the Netherlands
| | - Monique Nijhuis
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Annemarie M J Wensing
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
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22
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Antonelli M, Penfold RS, Merino J, Sudre CH, Molteni E, Berry S, Canas LS, Graham MS, Klaser K, Modat M, Murray B, Kerfoot E, Chen L, Deng J, Österdahl MF, Cheetham NJ, Drew DA, Nguyen LH, Pujol JC, Hu C, Selvachandran S, Polidori L, May A, Wolf J, Chan AT, Hammers A, Duncan EL, Spector TD, Ourselin S, Steves CJ. Risk factors and disease profile of post-vaccination SARS-CoV-2 infection in UK users of the COVID Symptom Study app: a prospective, community-based, nested, case-control study. THE LANCET. INFECTIOUS DISEASES 2022; 22:43-55. [PMID: 34480857 PMCID: PMC8409907 DOI: 10.1016/s1473-3099(21)00460-6] [Citation(s) in RCA: 452] [Impact Index Per Article: 226.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/20/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND COVID-19 vaccines show excellent efficacy in clinical trials and effectiveness in real-world data, but some people still become infected with SARS-CoV-2 after vaccination. This study aimed to identify risk factors for post-vaccination SARS-CoV-2 infection and describe the characteristics of post-vaccination illness. METHODS This prospective, community-based, nested, case-control study used self-reported data (eg, on demographics, geographical location, health risk factors, and COVID-19 test results, symptoms, and vaccinations) from UK-based, adult (≥18 years) users of the COVID Symptom Study mobile phone app. For the risk factor analysis, cases had received a first or second dose of a COVID-19 vaccine between Dec 8, 2020, and July 4, 2021; had either a positive COVID-19 test at least 14 days after their first vaccination (but before their second; cases 1) or a positive test at least 7 days after their second vaccination (cases 2); and had no positive test before vaccination. Two control groups were selected (who also had not tested positive for SARS-CoV-2 before vaccination): users reporting a negative test at least 14 days after their first vaccination but before their second (controls 1) and users reporting a negative test at least 7 days after their second vaccination (controls 2). Controls 1 and controls 2 were matched (1:1) with cases 1 and cases 2, respectively, by the date of the post-vaccination test, health-care worker status, and sex. In the disease profile analysis, we sub-selected participants from cases 1 and cases 2 who had used the app for at least 14 consecutive days after testing positive for SARS-CoV-2 (cases 3 and cases 4, respectively). Controls 3 and controls 4 were unvaccinated participants reporting a positive SARS-CoV-2 test who had used the app for at least 14 consecutive days after the test, and were matched (1:1) with cases 3 and 4, respectively, by the date of the positive test, health-care worker status, sex, body-mass index (BMI), and age. We used univariate logistic regression models (adjusted for age, BMI, and sex) to analyse the associations between risk factors and post-vaccination infection, and the associations of individual symptoms, overall disease duration, and disease severity with vaccination status. FINDINGS Between Dec 8, 2020, and July 4, 2021, 1 240 009 COVID Symptom Study app users reported a first vaccine dose, of whom 6030 (0·5%) subsequently tested positive for SARS-CoV-2 (cases 1), and 971 504 reported a second dose, of whom 2370 (0·2%) subsequently tested positive for SARS-CoV-2 (cases 2). In the risk factor analysis, frailty was associated with post-vaccination infection in older adults (≥60 years) after their first vaccine dose (odds ratio [OR] 1·93, 95% CI 1·50-2·48; p<0·0001), and individuals living in highly deprived areas had increased odds of post-vaccination infection following their first vaccine dose (OR 1·11, 95% CI 1·01-1·23; p=0·039). Individuals without obesity (BMI <30 kg/m2) had lower odds of infection following their first vaccine dose (OR 0·84, 95% CI 0·75-0·94; p=0·0030). For the disease profile analysis, 3825 users from cases 1 were included in cases 3 and 906 users from cases 2 were included in cases 4. Vaccination (compared with no vaccination) was associated with reduced odds of hospitalisation or having more than five symptoms in the first week of illness following the first or second dose, and long-duration (≥28 days) symptoms following the second dose. Almost all symptoms were reported less frequently in infected vaccinated individuals than in infected unvaccinated individuals, and vaccinated participants were more likely to be completely asymptomatic, especially if they were 60 years or older. INTERPRETATION To minimise SARS-CoV-2 infection, at-risk populations must be targeted in efforts to boost vaccine effectiveness and infection control measures. Our findings might support caution around relaxing physical distancing and other personal protective measures in the post-vaccination era, particularly around frail older adults and individuals living in more deprived areas, even if these individuals are vaccinated, and might have implications for strategies such as booster vaccinations. FUNDING ZOE, the UK Government Department of Health and Social Care, the Wellcome Trust, the UK Engineering and Physical Sciences Research Council, UK Research and Innovation London Medical Imaging and Artificial Intelligence Centre for Value Based Healthcare, the UK National Institute for Health Research, the UK Medical Research Council, the British Heart Foundation, and the Alzheimer's Society.
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Affiliation(s)
- Michela Antonelli
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Rose S Penfold
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK; Department of Ageing and Health, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Jordi Merino
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Programs in Metabolism, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Programs in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Carole H Sudre
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; MRC Unit for Lifelong Health and Ageing at UCL, University College London, London, UK; Centre for Medical Image Computing, University College London, London, UK
| | - Erika Molteni
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Sarah Berry
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Liane S Canas
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Mark S Graham
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Kerstin Klaser
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Marc Modat
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Benjamin Murray
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Eric Kerfoot
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Liyuan Chen
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Jie Deng
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Marc F Österdahl
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK; Department of Ageing and Health, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Nathan J Cheetham
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - David A Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Long H Nguyen
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | | | | | | | | | | | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alexander Hammers
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; King's College London and Guy's and St Thomas' PET Centre, London, UK
| | - Emma L Duncan
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK; Department of Endocrinology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Sebastien Ourselin
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK; Department of Ageing and Health, Guy's and St Thomas' NHS Foundation Trust, London, UK.
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23
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Benning L, Morath C, Bartenschlager M, Nusshag C, Kälble F, Buylaert M, Schaier M, Beimler J, Klein K, Grenz J, Reichel P, Hidmark A, Ponath G, Töllner M, Reineke M, Rieger S, Tönshoff B, Schnitzler P, Zeier M, Süsal C, Bartenschlager R, Speer C. Neutralization of SARS-CoV-2 Variants of Concern in Kidney Transplant Recipients after Standard COVID-19 Vaccination. Clin J Am Soc Nephrol 2022; 17:98-106. [PMID: 34937771 PMCID: PMC8763153 DOI: 10.2215/cjn.11820921] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/01/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND AND OBJECTIVES Antibody response after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination is impaired in kidney transplant recipients. Emerging variants, such as B.1.617.2 (δ), are of particular concern because of their higher transmissibility and partial immune escape. Little is known about protection against these variants in immunocompromised patients. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS In this prospective two-center study, antispike 1 IgG and surrogate neutralizing antibodies were measured in 173 kidney transplant recipients and 166 healthy controls with different vaccination schedules. In addition, different SARS-CoV-2 epitope antibodies from 135 vaccinated kidney transplant recipients were compared with antibodies in 25 matched healthy controls after second vaccination. In 36 kidney transplant recipients with seroconversion, neutralization against B.1.1.7 (α), B.1.351 (β), and B.1.617.2 (δ) was determined on VeroE6 cells and compared with neutralization in 25 healthy controls. RESULTS Kidney transplant recipients had significantly lower seroconversion rates compared with healthy controls. After the second vaccination, antispike 1, antireceptor-binding domain, and surrogate neutralizing antibodies were detectable in 30%, 27%, and 24% of kidney transplant recipients, respectively. This compares with 100%, 96%, and 100% in healthy controls, respectively (P<0.001). Neutralization against B.1.1.7 was detectable in all kidney transplant recipients with seroconversion, with a median serum dilution that reduces infection of cells by 50% of 80 (interquartile range, 80-320). In contrast, only 23 of 36 (64%) and 24 of 36 (67%) kidney transplant recipients showed neutralization against B.1.351 and B.1.617.2, respectively, with median serum dilutions that reduce infection of cells by 50% of 20 (interquartile range, 0-40) and 20 (interquartile range, 0-40), respectively. Neutralization against different variants was significantly higher in healthy controls (P<0.001), with all patients showing neutralization against all tested variants. CONCLUSIONS Seroconverted kidney transplant recipients show impaired neutralization against emerging variants of concern after standard two-dose vaccination. CLINICAL TRIAL REGISTRY NAME AND REGISTRATION NUMBER Observational study to assess the SARS-CoV-2 specific immune response in kidney transplant recipients (COVID-19 related immune response), DRKS00024668.
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Affiliation(s)
- Louise Benning
- Department of Nephrology, University of Heidelberg, Heidelberg, Germany
| | - Christian Morath
- Department of Nephrology, University of Heidelberg, Heidelberg, Germany
| | - Marie Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Christian Nusshag
- Department of Nephrology, University of Heidelberg, Heidelberg, Germany
| | - Florian Kälble
- Department of Nephrology, University of Heidelberg, Heidelberg, Germany
| | - Mirabel Buylaert
- Department of Nephrology, University of Heidelberg, Heidelberg, Germany
| | - Matthias Schaier
- Department of Nephrology, University of Heidelberg, Heidelberg, Germany
| | - Jörg Beimler
- Department of Nephrology, University of Heidelberg, Heidelberg, Germany
| | - Katrin Klein
- Department of Nephrology, University of Heidelberg, Heidelberg, Germany
| | - Julia Grenz
- Department of Nephrology, University of Heidelberg, Heidelberg, Germany
| | - Paula Reichel
- Department of Nephrology, University of Heidelberg, Heidelberg, Germany
| | - Asa Hidmark
- Department of Nephrology, University of Heidelberg, Heidelberg, Germany
| | - Gerald Ponath
- Department of Nephrology, University of Heidelberg, Heidelberg, Germany
| | | | - Marvin Reineke
- Department of Nephrology, University of Heidelberg, Heidelberg, Germany
| | - Susanne Rieger
- Department of Pediatrics I, University Children’s Hospital Heidelberg, Heidelberg, Germany
| | - Burkhard Tönshoff
- Department of Pediatrics I, University Children’s Hospital Heidelberg, Heidelberg, Germany
| | - Paul Schnitzler
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| | - Martin Zeier
- Department of Nephrology, University of Heidelberg, Heidelberg, Germany
| | - Caner Süsal
- Institute of Immunology, University of Heidelberg, Heidelberg, Germany,Transplant Immunology Research Center of Excellence, Koç Üniversitesi Hastanesi, Istanbul, Turkey
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany,German Center for Infection Research, Heidelberg Partner Site, Heidelberg, Germany,Division of Virus-Associated Carcinogenesis, German Cancer Research Center, Heidelberg, Germany
| | - Claudius Speer
- Department of Nephrology, University of Heidelberg, Heidelberg, Germany,Molecular Medicine Partnership Unit Heidelberg, European Molecular Biology Laboratory, Heidelberg, Germany
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24
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Acharya R, Kafle S, Kandinata N, Slipman B, Ghimire M, Trotter AB. A Retrospective Cross-Sectional Study of Severe Breakthrough SARS-CoV-2 Infection in the General Population Requiring Hospitalization Within a Single Health System. J Clin Med Res 2022; 14:45-52. [PMID: 35211216 PMCID: PMC8827223 DOI: 10.14740/jocmr4662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 01/20/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Despite coronavirus disease 2019 (COVID-19) vaccination efforts, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in vaccinated individuals ("breakthrough SARS-CoV-2 infections") have emerged. Our understanding of breakthrough SARS-CoV-2 infections continues to evolve, and there is a paucity of information describing severe breakthrough SARS-CoV-2 infections. We conducted this study with the aim of describing breakthrough SARS-CoV-2 infections requiring hospitalization and exploring factors associated with severe breakthrough infection. METHODS The study included patients within our health network who received at least one dose of a messenger RNA (mRNA) COVID-19 vaccine and required hospitalization due to breakthrough SARS-CoV-2 infection from January 1 to August 15, 2021. We performed a descriptive analysis of vaccinated patients requiring hospitalization. Multivariable logistic regression (LR) analysis was performed to explore factors associated with severe breakthrough infection. RESULTS Out of 67,223 vaccinated individuals, 78 (0.12%) patients were hospitalized with breakthrough SARS-CoV-2 infection, of which 25 individuals (0.04% of those vaccinated, and 32% of all hospitalized) developed severe infection. The mean age of those with breakthrough infection was 72 years, the majority were White (60%), and dyspnea was the most common reason for hospital admission (53%), with bimodal peaks of hospitalization in January-February (40%) and July-August (34%). In LR analysis, male patients had 4.03 times the odds of developing severe SARS-CoV-2 infection than female patients (adjusted odds ratio (aOR): 4.03, 95% confidence interval (CI): 1.21 - 13.40), and an immunocompromising condition had 6.32 times the odds of developing severe COVID-19 disease (aOR: 6.32, 95% CI: 1.48 - 26.18). CONCLUSIONS The rate of severe breakthrough SARS-CoV-2 infection was very low, and male sex and immunocompromising conditions were associated with severe breakthrough infection. Clinicians and health systems should continue to campaign for COVID-19 vaccination aggressively.
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Affiliation(s)
- Roshan Acharya
- Department of Internal Medicine, Cape Fear Valley Medical Center, Fayetteville, NC 28304, USA
| | - Smita Kafle
- Fayetteville State University School of Nursing, Fayetteville, NC 28301, USA
| | - Natalie Kandinata
- Department of Internal Medicine, Cape Fear Valley Medical Center, Fayetteville, NC 28304, USA
| | - Brian Slipman
- Department of Internal Medicine, Cape Fear Valley Medical Center, Fayetteville, NC 28304, USA
| | - Meera Ghimire
- Department of Internal Medicine, Cape Fear Valley Medical Center, Fayetteville, NC 28304, USA
| | - Andrew B. Trotter
- Division of Infectious Disease, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
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25
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Duerr R, Dimartino D, Marier C, Zappile P, Levine S, François F, Iturrate E, Wang G, Dittmann M, Lighter J, Elbel B, Troxel AB, Goldfeld KS, Heguy A. Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.12.07.21267431. [PMID: 34909779 PMCID: PMC8669846 DOI: 10.1101/2021.12.07.21267431] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In 2021, Delta has become the predominant SARS-CoV-2 variant worldwide. While vaccines effectively prevent COVID-19 hospitalization and death, vaccine breakthrough infections increasingly occur. The precise role of clinical and genomic determinants in Delta infections is not known, and whether they contribute to increased rates of breakthrough infections compared to unvaccinated controls. Here, we show a steep and near complete replacement of circulating variants with Delta between May and August 2021 in metropolitan New York. We observed an increase of the Delta sublineage AY.25, its spike mutation S112L, and nsp12 mutation F192V in breakthroughs. Delta infections were associated with younger age and lower hospitalization rates than Alpha. Delta breakthroughs increased significantly with time since vaccination, and, after adjusting for confounders, they rose at similar rates as in unvaccinated individuals. Our data indicate a limited impact of vaccine escape in favor of Delta's increased epidemic growth in times of waning vaccine protection.
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Affiliation(s)
- Ralf Duerr
- Department of Microbiology, NYU Grossman School of Medicine
| | - Dacia Dimartino
- Genome Technology Center, Office of Science and Research, NYU Langone Health
| | - Christian Marier
- Genome Technology Center, Office of Science and Research, NYU Langone Health
| | - Paul Zappile
- Genome Technology Center, Office of Science and Research, NYU Langone Health
| | | | | | | | - Guiqing Wang
- Department of Pathology, NYU Grossman School of Medicine
| | - Meike Dittmann
- Department of Microbiology, NYU Grossman School of Medicine
| | - Jennifer Lighter
- Department of Pediatric Infectious Diseases, NYU Grossman School of Medicine
| | - Brian Elbel
- Department of Population Health, NYU Grossman School of Medicine
- NYU Wagner Graduate School of Public Service
| | - Andrea B. Troxel
- Department of Population Health, NYU Grossman School of Medicine
| | | | - Adriana Heguy
- Genome Technology Center, Office of Science and Research, NYU Langone Health
- Department of Pathology, NYU Grossman School of Medicine
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26
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Olsen RJ, Christensen PA, Long SW, Subedi S, Hodjat P, Olson R, Nguyen M, Davis JJ, Yerramilli P, Saavedra MO, Pruitt L, Reppond K, Shyer MN, Cambric J, Gadd R, Thakur RM, Batajoo A, Finkelstein IJ, Gollihar J, Musser JM. Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. THE AMERICAN JOURNAL OF PATHOLOGY 2021; 191:1754-1773. [PMID: 34303698 PMCID: PMC8299152 DOI: 10.1016/j.ajpath.2021.07.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 12/13/2022]
Abstract
Certain genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are of substantial concern because they may be more transmissible or detrimentally alter the pandemic course and disease features in individual patients. SARS-CoV-2 genome sequences from 12,476 patients in the Houston Methodist health care system diagnosed from January 1 through May 31, 2021 are reported here. Prevalence of the B.1.1.7 (Alpha) variant increased rapidly and caused 63% to 90% of new cases in the latter half of May. Eleven B.1.1.7 genomes had an E484K replacement in spike protein, a change also identified in other SARS-CoV-2 lineages. Compared with non-B.1.1.7-infected patients, individuals with B.1.1.7 had a significantly lower cycle threshold (a proxy for higher virus load) and significantly higher hospitalization rate. Other variants [eg, B.1.429 and B.1.427 (Epsilon), P.1 (Gamma), P.2 (Zeta), and R.1] also increased rapidly, although the magnitude was less than that in B.1.1.7. Twenty-two patients infected with B.1.617.1 (Kappa) or B.1.617.2 (Delta) variants had a high rate of hospitalization. Breakthrough cases (n = 207) in fully vaccinated patients were caused by a heterogeneous array of virus genotypes, including many not currently designated variants of interest or concern. In the aggregate, this study delineates the trajectory of SARS-CoV-2 variants circulating in a major metropolitan area, documents B.1.1.7 as the major cause of new cases in Houston, TX, and heralds the arrival of B.1.617 variants in the metroplex.
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Affiliation(s)
- Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, New York, New York
| | - Paul A Christensen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - S Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, New York, New York
| | - Sishir Subedi
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Parsa Hodjat
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Robert Olson
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - James J Davis
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Prasanti Yerramilli
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Matthew O Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Layne Pruitt
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Kristina Reppond
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Madison N Shyer
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Jessica Cambric
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Ryan Gadd
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Rashi M Thakur
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Akanksha Batajoo
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute of Molecular Biosciences, The University of Texas at Austin, Austin, Texas
| | - Jimmy Gollihar
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Combat Capabilities Development Command (CCDC) Army Research Laboratory-South, University of Texas, Austin, Texas
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, New York, New York.
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27
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Amoah GB, Quakyi IA, Sagoe KW, Ayettey-Anie HNG, Ayettey-Adamafio MNB, Ayettey Brew RNA, Newman-Nartey M, Nartey NO, Brightson KTC, Kessie G, Ayettey AS, Konotey-Ahulu FID. Re: Oral antiseptics against coronavirus: in-vitro and clinical evidence. J Hosp Infect 2021; 118:108-109. [PMID: 34487774 PMCID: PMC8414839 DOI: 10.1016/j.jhin.2021.08.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/29/2021] [Indexed: 02/07/2023]
Affiliation(s)
- G B Amoah
- University of Ghana Medical School, College of Health Sciences, University of Ghana, Legon, Ghana
| | - I A Quakyi
- School of Public Health, College of Health Sciences, University of Ghana, Legon, Ghana
| | - K W Sagoe
- Department of Medical Microbiology, University of Ghana Medical School, College of Health Sciences, University of Ghana, Legon, Ghana.
| | - H N G Ayettey-Anie
- National Radiotherapy Oncology and Nuclear Medicine Centre, Korle Bu Teaching Hospital, Accra, Ghana
| | | | - R N A Ayettey Brew
- Department of Obstetrics and Gynecology, Korle Bu Teaching Hospital, Accra, Ghana
| | - M Newman-Nartey
- University of Ghana Dental School, College of Health Sciences, University of Ghana, Ghana
| | - N O Nartey
- University of Ghana Dental School, College of Health Sciences, University of Ghana, Ghana
| | | | - G Kessie
- Mount Olives Hospital (MO), Techiman, Bono East Region, Ghana
| | - A S Ayettey
- University of Ghana Medical School, College of Health Sciences, University of Ghana, Legon, Ghana
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28
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Rzymski P, Pazgan-Simon M, Simon K, Łapiński T, Zarębska-Michaluk D, Szczepańska B, Chojnicki M, Mozer-Lisewska I, Flisiak R. Clinical Characteristics of Hospitalized COVID-19 Patients Who Received at Least One Dose of COVID-19 Vaccine. Vaccines (Basel) 2021; 9:781. [PMID: 34358197 PMCID: PMC8310296 DOI: 10.3390/vaccines9070781] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 12/20/2022] Open
Abstract
The clinical trials of the COVID-19 vaccines that are authorized in the European Union have revealed high efficacy in preventing symptomatic infections. However, during vaccination campaigns, some vaccine recipients, including those partially and fully vaccinated, will experience severe COVID-19, requiring hospitalization. This may particularly concern patients with a diminished immune response to the vaccine, as well as non-responders. This work has retrospectively analyzed the 92 cases of patients who were hospitalized between 27 December 2020 and 31 May 2021 in four Polish healthcare units due to COVID-19, and who have previously received the COVID-19 vaccine (54.3% ≤ 14 days after the first dose, 26.1% > 14 days after the first dose, 7.6% ≤ 14 days after the second dose, and 12% > 14 days after the second dose). These patients represented a minute fraction (1.2%) of all the COVID-19 patients who were hospitalized during the same period in the same healthcare institutions. No significant differences in white blood count, absolute lymphocyte count nadir, C-reactive protein, interleukin-6, procalcitonin, oxygen saturation, lung involvement, and fever frequency were found between the recipients of the first and second vaccine dose. A total of 15 deaths were noted (1.1% of all fatal COVID-19 cases in the considered period and healthcare units), including six in patients who received the second dose (five > 14 days after the second dose)-three of these subjects were using immunosuppressive medicines, and two were confirmed to be vaccine non-responders. The study reassures that severe COVID-19 and deaths are not common in vaccinated individuals, highlights that the clinical course in such patients may not reveal any distinctive features, and advocates for close monitoring of those at a higher risk of vaccine failure.
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Affiliation(s)
- Piotr Rzymski
- Department of Environmental Medicine, Poznan University of Medical Sciences, 60-806 Poznań, Poland
- Integrated Science Association (ISA), Universal Scientific Education and Research Network (USERN), 60-806 Poznań, Poland
| | - Monika Pazgan-Simon
- 1st Infectious Diseases Ward, Gromkowski Regional Specialist Hospital, 50-149 Wroclaw, Poland;
- Department of Infectious Diseases and Hepatology, Wrocław Medical University, 51-149 Wrocław, Poland;
| | - Krzysztof Simon
- Department of Infectious Diseases and Hepatology, Wrocław Medical University, 51-149 Wrocław, Poland;
| | - Tadeusz Łapiński
- Department of Infectious Diseases and Hepatology, Medical University of Bialystok, 15-540 Białystok, Poland;
| | | | - Barbara Szczepańska
- Department of the Children’s Diseases, The Infectious-Neurological Subdivision, Jan Kochanowski University, 25-369 Kielce, Poland;
| | - Michał Chojnicki
- Department of Immunobiology, Poznan University of Medical Sciences, 60-806 Poznań, Poland;
- Department of Infectious Diseases, Jozef Strus Hospital, 61-285 Poznań, Poland;
| | | | - Robert Flisiak
- Department of Infectious Diseases and Hepatology, Medical University of Bialystok, 15-540 Białystok, Poland;
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29
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Marques AD, Sherrill-Mix S, Everett JK, Reddy S, Hokama P, Roche AM, Hwang Y, Glascock A, Whiteside SA, Graham-Wooten J, Khatib LA, Fitzgerald AS, Moustafa AM, Bianco C, Rajagopal S, Helton J, Deming R, Denu L, Ahmed A, Kitt E, Coffin SE, Newbern C, Mell JC, Planet PJ, Badjatia N, Richards B, Wang ZX, Cannuscio CC, Strelau KM, Jaskowiak-Barr A, Cressman L, Loughrey S, Ganguly A, Feldman MD, Collman RG, Rodino KG, Kelly BJ, Bushman FD. SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021. mBio 2021; 13:e0378821. [PMID: 35130727 PMCID: PMC8942461 DOI: 10.1128/mbio.03788-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/12/2022] [Indexed: 12/29/2022] Open
Abstract
The severe acute respiratory coronavirus-2 (SARS-CoV-2) is the cause of the global outbreak of COVID-19. Evidence suggests that the virus is evolving to allow efficient spread through the human population, including vaccinated individuals. Here, we report a study of viral variants from surveillance of the Delaware Valley, including the city of Philadelphia, and variants infecting vaccinated subjects. We sequenced and analyzed complete viral genomes from 2621 surveillance samples from March 2020 to September 2021 and compared them to genome sequences from 159 vaccine breakthroughs. In the early spring of 2020, all detected variants were of the B.1 and closely related lineages. A mixture of lineages followed, notably including B.1.243 followed by B.1.1.7 (alpha), with other lineages present at lower levels. Later isolations were dominated by B.1.617.2 (delta) and other delta lineages; delta was the exclusive variant present by the last time sampled. To investigate whether any variants appeared preferentially in vaccine breakthroughs, we devised a model based on Bayesian autoregressive moving average logistic multinomial regression to allow rigorous comparison. This revealed that B.1.617.2 (delta) showed 3-fold enrichment in vaccine breakthrough cases (odds ratio of 3; 95% credible interval 0.89-11). Viral point substitutions could also be associated with vaccine breakthroughs, notably the N501Y substitution found in the alpha, beta and gamma variants (odds ratio 2.04; 95% credible interval of1.25-3.18). This study thus overviews viral evolution and vaccine breakthroughs in the Delaware Valley and introduces a rigorous statistical approach to interrogating enrichment of breakthrough variants against a changing background. IMPORTANCE SARS-CoV-2 vaccination is highly effective at reducing viral infection, hospitalization and death. However, vaccine breakthrough infections have been widely observed, raising the question of whether particular viral variants or viral mutations are associated with breakthrough. Here, we report analysis of 2621 surveillance isolates from people diagnosed with COVID-19 in the Delaware Valley in southeastern Pennsylvania, allowing rigorous comparison to 159 vaccine breakthrough case specimens. Our best estimate is a 3-fold enrichment for some lineages of delta among breakthroughs, and enrichment of a notable spike substitution, N501Y. We introduce statistical methods that should be widely useful for evaluating vaccine breakthroughs and other viral phenotypes.
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Affiliation(s)
- Andrew D. Marques
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Scott Sherrill-Mix
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John K. Everett
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Shantan Reddy
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Pascha Hokama
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Aoife M. Roche
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Young Hwang
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Abigail Glascock
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Samantha A. Whiteside
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Jevon Graham-Wooten
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Layla A. Khatib
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ayannah S. Fitzgerald
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ahmed M. Moustafa
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Gastroenterology, Hepatology & Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Colleen Bianco
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Swetha Rajagopal
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jenna Helton
- Division of COVID-19 Containment, Philadelphia Department of Public Health, Philadelphia, Pennsylvania, USA
| | - Regan Deming
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lidiya Denu
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Azad Ahmed
- Department of Microbiology & Immunology, Center for Genomic Sciences, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Eimear Kitt
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Susan E. Coffin
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Claire Newbern
- Division of COVID-19 Containment, Philadelphia Department of Public Health, Philadelphia, Pennsylvania, USA
| | - Josh Chang Mell
- Department of Microbiology & Immunology, Center for Genomic Sciences, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Paul J. Planet
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Nitika Badjatia
- Molecular & Genomic Pathology Laboratory, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania, USA
| | - Bonnie Richards
- Jefferson Occupational Health Network for Employees and Students (JOHN), Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Zi-Xuan Wang
- Molecular & Genomic Pathology Laboratory, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania, USA
- Department of Anatomy, Pathology, and Cell Biology, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania, USA
| | - Carolyn C. Cannuscio
- Leonard Davis Institute of Health Economics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Family Medicine and Community Health, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Katherine M. Strelau
- Leonard Davis Institute of Health Economics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Family Medicine and Community Health, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anne Jaskowiak-Barr
- Division of Infectious Diseases, Department of Medicine & Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Leigh Cressman
- Division of Infectious Diseases, Department of Medicine & Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sean Loughrey
- Division of Infectious Diseases, Department of Medicine & Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Arupa Ganguly
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael D. Feldman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ronald G. Collman
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Kyle G. Rodino
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Brendan J. Kelly
- Division of Infectious Diseases, Department of Medicine & Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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