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Zhao XJ, Ji B, Shang C, Li DY, Zhang S, Gu HJ, Peng HH, Qian C, Zhang CL, Shi C, Shen Y, Chen JJ, Xu Q, Lv CL, Jiang BG, Wang H, Li X, Wang GL, Fang LQ. Humoral and cellular immune responses following Omicron BA.2.2 breakthrough infection and Omicron BA.5 reinfection. iScience 2024; 27:110283. [PMID: 39040063 PMCID: PMC11260851 DOI: 10.1016/j.isci.2024.110283] [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: 12/11/2023] [Revised: 04/23/2024] [Accepted: 06/13/2024] [Indexed: 07/24/2024] Open
Abstract
The emergence of novel Omicron subvariants has raised concerns regarding the efficacy of immunity induced by prior Omicron subvariants breakthrough infection (BTI) or reinfection against current circulating Omicron subvariants. Here, we prospectively investigated the durability of antibody and T cell responses in individuals post Omicron BA.2.2 BTI, with or without subsequent Omicron BA.5 reinfection. Our findings reveal that the emerging Omicron subvariants, including CH.1.1, XBB, and JN.1, exhibit extensive immune evasion induced by previous infections. Notably, the level of IgG and neutralizing antibodies were found to correlate with subsequent Omicron BA.5 reinfection. Fortunately, T cell responses recognizing both Omicron BA.2 and CH.1.1 peptides were observed. Furthermore, Omicron BA.5 reinfection may alleviate immune imprinting induced by WT-vaccination, bolster virus-specific ICS+ T cell responses, and promote the phenotypic differentiation of virus-specific memory CD8+ T cells. Antigen-updated or T cell-conserved vaccines are needed to control the transmission of diverse emerging SARS-CoV-2 variants.
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Affiliation(s)
- Xin-Jing Zhao
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Science, Beijing, P.R. China
| | - Bin Ji
- Department of Disease Control, the Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, China
| | - Chao Shang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - De-Yu Li
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Science, Beijing, P.R. China
| | - Sheng Zhang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Science, Beijing, P.R. China
| | - Hong-Jing Gu
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Science, Beijing, P.R. China
| | - Hong-Hong Peng
- Department of Disease Control, the Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, China
| | - Cheng Qian
- Jiangyin Center for Disease Control and Prevention, Jiangyin, China
| | - Cui-Ling Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Chao Shi
- Department of Disease Control, the Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, China
| | - Yuan Shen
- Department of Disease Control, the Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, China
| | - Jin-Jin Chen
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Science, Beijing, P.R. China
| | - Qiang Xu
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Science, Beijing, P.R. China
| | - Chen-Long Lv
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Science, Beijing, P.R. China
| | - Bao-Gui Jiang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Science, Beijing, P.R. China
| | - Hui Wang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Science, Beijing, P.R. China
| | - Xiao Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Guo-Lin Wang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Science, Beijing, P.R. China
| | - Li-Qun Fang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Science, Beijing, P.R. China
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Li Y, Choudhary MC, Regan J, Boucau J, Nathan A, Speidel T, Liew MY, Edelstein GE, Kawano Y, Uddin R, Deo R, Marino C, Getz MA, Reynolds Z, Barry M, Gilbert RF, Tien D, Sagar S, Vyas TD, Flynn JP, Hammond SP, Novack LA, Choi B, Cernadas M, Wallace ZS, Sparks JA, Vyas JM, Seaman MS, Gaiha GD, Siedner MJ, Barczak AK, Lemieux JE, Li JZ. SARS-CoV-2 viral clearance and evolution varies by type and severity of immunodeficiency. Sci Transl Med 2024; 16:eadk1599. [PMID: 38266109 PMCID: PMC10982957 DOI: 10.1126/scitranslmed.adk1599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 12/18/2023] [Indexed: 01/26/2024]
Abstract
Despite vaccination and antiviral therapies, immunocompromised individuals are at risk for prolonged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but the immune defects that predispose an individual to persistent coronavirus disease 2019 (COVID-19) remain incompletely understood. In this study, we performed detailed viro-immunologic analyses of a prospective cohort of participants with COVID-19. The median times to nasal viral RNA and culture clearance in individuals with severe immunosuppression due to hematologic malignancy or transplant (S-HT) were 72 and 40 days, respectively, both of which were significantly longer than clearance rates in individuals with severe immunosuppression due to autoimmunity or B cell deficiency (S-A), individuals with nonsevere immunodeficiency, and nonimmunocompromised groups (P < 0.01). Participants who were severely immunocompromised had greater SARS-CoV-2 evolution and a higher risk of developing resistance against therapeutic monoclonal antibodies. Both S-HT and S-A participants had diminished SARS-CoV-2-specific humoral responses, whereas only the S-HT group had reduced T cell-mediated responses. This highlights the varied risk of persistent COVID-19 across distinct immunosuppressive conditions and suggests that suppression of both B and T cell responses results in the highest contributing risk of persistent infection.
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Affiliation(s)
- Yijia Li
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Manish C. Choudhary
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - James Regan
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Julie Boucau
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Anusha Nathan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Program in Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Boston, MA 02115, USA
| | - Tessa Speidel
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - May Yee Liew
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gregory E. Edelstein
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yumeko Kawano
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rockib Uddin
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rinki Deo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Caitlin Marino
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Matthew A. Getz
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Zahra Reynolds
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Mamadou Barry
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Rebecca F. Gilbert
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Dessie Tien
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Shruti Sagar
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Tammy D. Vyas
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - James P. Flynn
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah P. Hammond
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lewis A. Novack
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Bina Choi
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Manuela Cernadas
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Zachary S. Wallace
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jeffrey A. Sparks
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jatin M. Vyas
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Michael S. Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Gaurav D. Gaiha
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Mark J. Siedner
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Amy K. Barczak
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jacob E. Lemieux
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jonathan Z. Li
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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Nurisyah S, Iyori M, Hasyim AA, Sakamoto A, Hashimoto H, Yamagata K, Yamauchi S, Amru K, Zainal KH, Idris I, Yoshida S, Djaharuddin I, Syafruddin D, Bukhari A, Asih PBS, Yusuf Y. Comparison between Neutralization Capacity of Antibodies Elicited by COVID-19 Natural Infection and Vaccination in Indonesia: A Prospective Cohort. Antibodies (Basel) 2023; 12:60. [PMID: 37753974 PMCID: PMC10526084 DOI: 10.3390/antib12030060] [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: 08/01/2023] [Revised: 08/21/2023] [Accepted: 09/18/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND To fight the COVID-19 pandemic, immunity against SARS-CoV-2 should be achieved not only through natural infection but also by vaccination. The effect of COVID-19 vaccination on previously infected persons is debatable. METHODS A prospective cohort was undergone to collect sera from unvaccinated survivors and vaccinated persons-with and without COVID-19 pre-infection. The sera were analyzed for the anti-receptor binding domain (RBD) titers by ELISA and for the capacity to neutralize the pseudovirus of the Wuhan-Hu-1 strain by luciferase assays. RESULTS Neither the antibody titers nor the neutralization capacity was significantly different between the three groups. However, the correlation between the antibody titers and the percentage of viral neutralization derived from sera of unvaccinated survivors was higher than that from vaccinated persons with pre-infection and vaccinated naïve individuals (Spearman correlation coefficient (r) = -0.8558; 95% CI, -0.9259 to -0.7288), p < 0.0001 vs. -0.7855; 95% CI, -0.8877 to -0.6096, p < 0.0001 and -0.581; 95% CI, -0.7679 to -0.3028, p = 0.0002, respectively), indicating the capacity to neutralize the virus is most superior by infection alone. CONCLUSIONS Vaccines induce anti-RBD titers as high as the natural infection with lower neutralization capacity, and it does not boost immunity in pre-infected persons.
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Affiliation(s)
- Sitti Nurisyah
- Faculty of Medicine, Hasanuddin University, Makassar 90245, Indonesia; (S.N.); (K.A.); (I.I.); (I.D.); (D.S.); (A.B.)
- Dr. Tadjuddin Chalid Hospital, Makassar 90241, Indonesia
| | - Mitsuhiro Iyori
- Research Institute of Pharmaceutical Sciences, Musashino University, Nishitokyo, Tokyo 202-8585, Japan;
| | - Ammar Abdurrahman Hasyim
- Laboratory of Vaccinology and Applied Immunology, Kanazawa University, Kanazawa 920-1192, Japan; (A.A.H.); (A.S.); (H.H.); (K.Y.); (S.Y.); (K.H.Z.); (S.Y.)
| | - Akihiko Sakamoto
- Laboratory of Vaccinology and Applied Immunology, Kanazawa University, Kanazawa 920-1192, Japan; (A.A.H.); (A.S.); (H.H.); (K.Y.); (S.Y.); (K.H.Z.); (S.Y.)
| | - Hinata Hashimoto
- Laboratory of Vaccinology and Applied Immunology, Kanazawa University, Kanazawa 920-1192, Japan; (A.A.H.); (A.S.); (H.H.); (K.Y.); (S.Y.); (K.H.Z.); (S.Y.)
| | - Kyouhei Yamagata
- Laboratory of Vaccinology and Applied Immunology, Kanazawa University, Kanazawa 920-1192, Japan; (A.A.H.); (A.S.); (H.H.); (K.Y.); (S.Y.); (K.H.Z.); (S.Y.)
| | - Saya Yamauchi
- Laboratory of Vaccinology and Applied Immunology, Kanazawa University, Kanazawa 920-1192, Japan; (A.A.H.); (A.S.); (H.H.); (K.Y.); (S.Y.); (K.H.Z.); (S.Y.)
| | - Khaeriah Amru
- Faculty of Medicine, Hasanuddin University, Makassar 90245, Indonesia; (S.N.); (K.A.); (I.I.); (I.D.); (D.S.); (A.B.)
- Dr. Tadjuddin Chalid Hospital, Makassar 90241, Indonesia
| | - Kartika Hardianti Zainal
- Laboratory of Vaccinology and Applied Immunology, Kanazawa University, Kanazawa 920-1192, Japan; (A.A.H.); (A.S.); (H.H.); (K.Y.); (S.Y.); (K.H.Z.); (S.Y.)
| | - Irfan Idris
- Faculty of Medicine, Hasanuddin University, Makassar 90245, Indonesia; (S.N.); (K.A.); (I.I.); (I.D.); (D.S.); (A.B.)
- Hasanuddin University Medical Research Centre, Makassar 90245, Indonesia
| | - Shigeto Yoshida
- Laboratory of Vaccinology and Applied Immunology, Kanazawa University, Kanazawa 920-1192, Japan; (A.A.H.); (A.S.); (H.H.); (K.Y.); (S.Y.); (K.H.Z.); (S.Y.)
| | - Irawaty Djaharuddin
- Faculty of Medicine, Hasanuddin University, Makassar 90245, Indonesia; (S.N.); (K.A.); (I.I.); (I.D.); (D.S.); (A.B.)
- Dr. Wahidin Soedirohusodo Hospital, Makassar 90425, Indonesia
| | - Din Syafruddin
- Faculty of Medicine, Hasanuddin University, Makassar 90245, Indonesia; (S.N.); (K.A.); (I.I.); (I.D.); (D.S.); (A.B.)
- Hasanuddin University Medical Research Centre, Makassar 90245, Indonesia
| | - Agussalim Bukhari
- Faculty of Medicine, Hasanuddin University, Makassar 90245, Indonesia; (S.N.); (K.A.); (I.I.); (I.D.); (D.S.); (A.B.)
| | - Puji Budi Setia Asih
- Badan Riset dan Inovasi Nasional (National Research and Innovation Agency), Jakarta 10340, Indonesia;
| | - Yenni Yusuf
- Faculty of Medicine, Hasanuddin University, Makassar 90245, Indonesia; (S.N.); (K.A.); (I.I.); (I.D.); (D.S.); (A.B.)
- Hasanuddin University Medical Research Centre, Makassar 90245, Indonesia
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Lin YCJ, Evans DH, Robbins NF, Orjuela G, Abe KT, Rathod B, Colwill K, Gingras AC, Tuite A, Yi QL, O’Brien SF, Drews SJ. Diminished Neutralization Capacity of SARS-CoV-2 Omicron BA.1 in Donor Plasma Collected from January to March 2021. Microbiol Spectr 2023; 11:e0525622. [PMID: 37289096 PMCID: PMC10434250 DOI: 10.1128/spectrum.05256-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/25/2023] [Indexed: 06/09/2023] Open
Abstract
The 50% plaque reduction neutralization assay (PRNT50) has been previously used to assess the neutralization capacity of donor plasma against wild-type and variant of concern (VOC) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Emerging data suggest that plasma with an anti-SARS-CoV-2 level of ≥2 × 104 binding antibody units/mL (BAU/mL) protects against SARS-CoV-2 Omicron BA.1 infection. Specimens were collected using a cross-sectional random sampling approach. For PRNT50 studies, 63 previously analyzed specimens by PRNT50 versus SARS-CoV-2 wild-type, Alpha, Beta, Gamma, and Delta were analyzed by PRNT50 versus Omicron BA.1. The 63 specimens plus 4,390 specimens (randomly sampled regardless of serological evidence of infection) were also tested using the Abbott SARS-CoV-2 IgG II Quant assay (anti-spike [S]; Abbott, Chicago, IL, USA; Abbott Quant assay). In the vaccinated group, the percentages of specimens with any measurable PRNT50 versus wild-type or VOC were wild type (21/25 [84%]), Alpha (19/25 [76%]), Beta (18/25 [72%]), Gamma (13/25 [52%]), Delta (19/25 [76%]), and Omicron BA.1 (9/25 [36%]). In the unvaccinated group, the percentages of specimens with any measurable PRNT50 versus wild type or VOC were wild-type SARS-CoV-2 (16/39 [41%]), Alpha (16/39 [41%]), Beta (10/39 [26%]), Gamma (9/39 [23%]), Delta (16/39 [41%]), and Omicron BA.1 (0/39) (Fisher's exact tests, vaccinated versus unvaccinated for each variant, P < 0.05). None of the 4,453 specimens tested by the Abbott Quant assay had a binding capacity of ≥2 × 104 BAU/mL. Vaccinated donors were more likely than unvaccinated donors to neutralize Omicron when assessed by a PRNT50 assay. IMPORTANCE SARS-CoV-2 Omicron emergence occurred in Canada during the period from November 2021 to January 2022. This study assessed the ability of donor plasma collected earlier (January to March 2021) to generate any neutralizing capacity against Omicron BA.1 SARS-CoV-2. Vaccinated individuals, regardless of infection status, were more likely to neutralize Omicron BA.1 than unvaccinated individuals. This study then used a semiquantitative binding antibody assay to screen a larger number of specimens (4,453) for individual specimens that might have high-titer neutralizing capacity against Omicron BA.1. None of the 4,453 specimens tested by the semiquantitative SARS-CoV-2 assay had a binding capacity suggestive of a high-titer neutralizing capacity against Omicron BA.1. These data do not imply that Canadians lacked immunity to Omicron BA.1 during the study period. Immunity to SARS-CoV-2 is complex, and there is still no wide consensus on correlation of protection to SARS-CoV-2.
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Affiliation(s)
- Yi-Chan J. Lin
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Canada
| | - David H. Evans
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Canada
| | | | | | - Kento T. Abe
- Lunenfeld-Tanenbaum Research Institute at Mt. Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Bhavisha Rathod
- Lunenfeld-Tanenbaum Research Institute at Mt. Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Karen Colwill
- Lunenfeld-Tanenbaum Research Institute at Mt. Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute at Mt. Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ashleigh Tuite
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Qi-Long Yi
- Epidemiology and Surveillance, Canadian Blood Services, Ottawa, Ontario, Canada
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Sheila F. O’Brien
- Epidemiology and Surveillance, Canadian Blood Services, Ottawa, Ontario, Canada
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Steven J. Drews
- Canadian Blood Services, Microbiology, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
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5
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Li Y, Choudhary MC, Regan J, Boucau J, Nathan A, Speidel T, Liew MY, Edelstein GE, Kawano Y, Uddin R, Deo R, Marino C, Getz MA, Reynold Z, Barry M, Gilbert RF, Tien D, Sagar S, Vyas TD, Flynn JP, Hammond SP, Novack LA, Choi B, Cernadas M, Wallace ZS, Sparks JA, Vyas JM, Seaman MS, Gaiha GD, Siedner MJ, Barczak AK, Lemieux JE, Li JZ. SARS-CoV-2 Viral Clearance and Evolution Varies by Extent of Immunodeficiency. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.07.31.23293441. [PMID: 37577493 PMCID: PMC10418302 DOI: 10.1101/2023.07.31.23293441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Despite vaccination and antiviral therapies, immunocompromised individuals are at risk for prolonged SARS-CoV-2 infection, but the immune defects that predispose to persistent COVID-19 remain incompletely understood. In this study, we performed detailed viro-immunologic analyses of a prospective cohort of participants with COVID-19. The median time to nasal viral RNA and culture clearance in the severe hematologic malignancy/transplant group (S-HT) were 72 and 40 days, respectively, which were significantly longer than clearance rates in the severe autoimmune/B-cell deficient (S-A), non-severe, and non-immunocompromised groups (P<0.001). Participants who were severely immunocompromised had greater SARS-CoV-2 evolution and a higher risk of developing antiviral treatment resistance. Both S-HT and S-A participants had diminished SARS-CoV-2-specific humoral, while only the S-HT group had reduced T cell-mediated responses. This highlights the varied risk of persistent COVID-19 across immunosuppressive conditions and suggests that suppression of both B and T cell responses results in the highest contributing risk of persistent infection.
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Affiliation(s)
- Yijia Li
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Manish C Choudhary
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - James Regan
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Julie Boucau
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Anusha Nathan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Program in Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Boston, MA 02115, USA
| | - Tessa Speidel
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - May Yee Liew
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gregory E Edelstein
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yumeko Kawano
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rockib Uddin
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rinki Deo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Caitlin Marino
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Matthew A Getz
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Zahra Reynold
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Mamadou Barry
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Rebecca F Gilbert
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Dessie Tien
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Shruti Sagar
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tammy D Vyas
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - James P Flynn
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sarah P Hammond
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lewis A Novack
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Bina Choi
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Manuela Cernadas
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zachary S Wallace
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jeffrey A Sparks
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jatin M Vyas
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Gaurav D Gaiha
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Mark J Siedner
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Amy K Barczak
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Jacob E Lemieux
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan Z Li
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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Santos da Silva E, Servais JY, Kohnen M, Arendt V, Gilson G, Staub T, Seguin-Devaux C, Perez-Bercoff D. Vaccine- and Breakthrough Infection-Elicited Pre-Omicron Immunity More Effectively Neutralizes Omicron BA.1, BA.2, BA.4 and BA.5 Than Pre-Omicron Infection Alone. Curr Issues Mol Biol 2023; 45:1741-1761. [PMID: 36826057 PMCID: PMC9955496 DOI: 10.3390/cimb45020112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Since the emergence of SARS-CoV-2 Omicron BA.1 and BA.2, several Omicron sublineages have emerged, supplanting their predecessors. Here we compared the neutralization of Omicron sublineages BA.1, BA.2, BA.4 and BA.5 by human sera collected from individuals who were infected with the ancestral B.1 (D614G) strain, who were vaccinated (3 doses) or with breakthrough infection with pre-Omicron strains (Gamma or Delta). All Omicron sublineages exhibited extensive escape from all sera when compared to the ancestral B.1 strain and to Delta, albeit to different levels depending on the origin of the sera. Convalescent sera were unable to neutralize BA.1, and partly neutralized BA.2, BA.4 and BA.5. Vaccinee sera partly neutralized BA.2, but BA.1, BA.4 and BA.5 evaded neutralizing antibodies (NAb). Some breakthrough infections (BTI) sera were non-neutralizing. Neutralizing BTI sera had similar neutralizing ability against all Omicron sublineages. Despite similar levels of anti-Spike and anti-Receptor Binding Domain (RBD) antibodies in all groups, BTI sera had the highest cross-neutralizing ability against all Omicron sublineages and convalescent sera were the least neutralizing. Antibody avidity inferred from the NT50:antibody titer ratio was highest in sera from BTI patients, underscoring qualitative differences in antibodies elicited by infection or vaccination. Together, these findings highlight the importance of vaccination to trigger highly cross-reactive antibodies that neutralize phylogenetically and antigenically distant strains, and suggest that immune imprinting by first generation vaccines may restrict, but not abolish, cross-neutralization.
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Affiliation(s)
- Eveline Santos da Silva
- HIV Clinical and Translational Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg
| | - Jean-Yves Servais
- HIV Clinical and Translational Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg
| | - Michel Kohnen
- Centre Hospitalier de Luxembourg, 4 Rue Ernest Barblé, L-1210 Luxembourg, Luxembourg
| | - Victor Arendt
- Centre Hospitalier de Luxembourg, 4 Rue Ernest Barblé, L-1210 Luxembourg, Luxembourg
| | - Georges Gilson
- Centre Hospitalier de Luxembourg, 4 Rue Ernest Barblé, L-1210 Luxembourg, Luxembourg
| | - Therese Staub
- Centre Hospitalier de Luxembourg, 4 Rue Ernest Barblé, L-1210 Luxembourg, Luxembourg
| | - Carole Seguin-Devaux
- HIV Clinical and Translational Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg
| | - Danielle Perez-Bercoff
- HIV Clinical and Translational Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg
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Rössler A, Netzl A, Knabl L, Schäfer H, Wilks SH, Bante D, Falkensammer B, Borena W, von Laer D, Smith DJ, Kimpel J. BA.2 and BA.5 omicron differ immunologically from both BA.1 omicron and pre-omicron variants. Nat Commun 2022; 13:7701. [PMID: 36513653 PMCID: PMC9745279 DOI: 10.1038/s41467-022-35312-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
Several studies have shown that SARS-CoV-2 BA.1 omicron is an immune escape variant. Meanwhile, however, omicron BA.2 and BA.5 became dominant in many countries and replaced BA.1. As both have several mutations compared to BA.1, we analyzed whether BA.2 and BA.5 show further immune escape relative to BA.1. Here, we characterized neutralization profiles against the BA.2 and BA.5 omicron sub-variants in plasma samples from individuals with different history of exposures to infection/vaccination and found that unvaccinated individuals after a single exposure to BA.2 had limited cross-neutralizing antibodies to pre-omicron variants and to BA.1. Consequently, our antigenic map including all Variants of Concern and BA.1, BA.2 and BA.5 omicron sub-variants, showed that all omicron sub-variants are distinct to pre-omicron variants, but that the three omicron variants are also antigenically distinct from each other. The antibody landscapes illustrate that cross-neutralizing antibodies against the current antigenic space, as described in our maps, are generated only after three or more exposures to antigenically close variants but also after two exposures to antigenically distant variants. Here, we describe the antigenic space inhabited by the relevant SARS-CoV-2 variants, the understanding of which will have important implications for further vaccine strain adaptations.
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Affiliation(s)
- Annika Rössler
- grid.5361.10000 0000 8853 2677Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Antonia Netzl
- grid.5335.00000000121885934University of Cambridge, Center for Pathogen Evolution, Department of Zoology, Cambridge, UK
| | - Ludwig Knabl
- Tyrolpath Obrist Brunhuber GmbH, Hauptplatz 4, 6511 Zams, Austria
| | - Helena Schäfer
- grid.5361.10000 0000 8853 2677Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Samuel H. Wilks
- grid.5335.00000000121885934University of Cambridge, Center for Pathogen Evolution, Department of Zoology, Cambridge, UK
| | - David Bante
- grid.5361.10000 0000 8853 2677Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Barbara Falkensammer
- grid.5361.10000 0000 8853 2677Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Wegene Borena
- grid.5361.10000 0000 8853 2677Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Dorothee von Laer
- grid.5361.10000 0000 8853 2677Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Derek J. Smith
- grid.5335.00000000121885934University of Cambridge, Center for Pathogen Evolution, Department of Zoology, Cambridge, UK
| | - Janine Kimpel
- grid.5361.10000 0000 8853 2677Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
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Liu H, Varvel S, Chen G, McConnell J, Caffrey R, Galdzicka M, Shabahang S. Simultaneous measurement of multiple variant-specific SARS-CoV-2 neutralizing antibodies with a multiplexed flow cytometric assay. Front Immunol 2022; 13:1039163. [PMID: 36505453 PMCID: PMC9732243 DOI: 10.3389/fimmu.2022.1039163] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/31/2022] [Indexed: 11/27/2022] Open
Abstract
Introduction Neutralizing antibodies (NAbs) have been recognized as surrogates of protection against SARS-CoV-2; however, the emergence of variants/subvariants escaping neutralization suggests that laboratory assessments of NAbs against the ancestral/wild type (WT) antigens likely overestimate the degree of protection. Methods A novel flow cytometry-based multiplex test system was developed for the simultaneous detection of NAbs of multiple SARS-CoV-2 variants. SARS-CoV-2 antibodies (Abs) including IgG, IgM, IgA isotypes were measured in the same system. Samples from negative, convalesced, vaccinated, boosted, and breakthrough infection (BTI) populations were tested for both NAbs and Abs. Results NAbs induced by WT showed neutralization activity that correlated strongly to all variants (R2 > 0.85) except omicron BA.1/BA.2 (R2 <0.50). Two doses of vaccine elicited very little protective immunity against BA.1/BA.2, though a booster dose significantly improved NAbs for all variants. NAbs/Abs increased more following BTI than after a booster, suggesting that hybrid immunity (vaccination + natural immunity) was more robust to all variants including BA.1/BA.2. BTIs occurring in the omicron era led to stronger NAb responses against BA.1/BA.2 than did older BTIs. In all comparisons, the RBD antigens demonstrated greater differences between WT and BA.1/BA.2 than the spike antigens. Discussion Taken together, we demonstrated that both Ab and NAb against multiple SARS-CoV-2 variants/subvariants can be reliably detected on the same multiplex platform. Distinguishing NAbs to the appropriate antigenic target of prevalent variants offers the best correlate of protection and aids individual decisions about the appropriateness and cadence of vaccine boosters and other exposure mitigation strategies.
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Brazer N, Morris MK, Servellita V, Anglin K, Saldhi P, Garcia-Knight M, Bethancourt S, Sotomayor-Gonzalez A, Wang B, Foresythe A, Nguyen J, Gliwa AS, Pineda-Ramirez J, Sanchez RD, Zhang Y, Ott M, Wadford DA, Andino R, Kelly JD, Hanson C, Chiu C. Neutralizing Immunity Induced Against the Omicron BA.1 and BA.2 Variants in Vaccine Breakthrough Infections. J Infect Dis 2022; 226:1688-1698. [PMID: 36134603 PMCID: PMC9619439 DOI: 10.1093/infdis/jiac384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/10/2022] [Accepted: 09/20/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND As of early 2022, the Omicron variants are the predominant circulating lineages globally. Understanding neutralizing antibody responses against Omicron BA.1 and BA.2 after vaccine breakthrough infections will provide insights into BA.2 infectivity and susceptibility to subsequent reinfection. METHODS Live virus neutralization assays were used to study immunity against Delta and Omicron BA.1 and BA.2 variants in samples from 86 individuals, 24 unvaccinated (27.9%) and 62 vaccinated (72.1%), who were infected with Delta (n = 42, 48.8%) or BA.1 (n = 44, 51.2%). Among the 62 vaccinated individuals, 39 were unboosted (62.9%), whereas 23 were boosted (37.1%). RESULTS In unvaccinated infections, neutralizing antibodies (nAbs) against the three variants were weak or undetectable, except against Delta for Delta-infected individuals. Both Delta and BA.1 breakthrough infections resulted in strong nAb responses against ancestral wild-type and Delta lineages, but moderate nAb responses against BA.1 and BA.2, with similar titers between unboosted and boosted individuals. Antibody titers against BA.2 were generally higher than those against BA.1 in breakthrough infections. CONCLUSIONS These results underscore the decreased immunogenicity of BA.1 compared to BA.2, insufficient neutralizing immunity against BA.2 in unvaccinated individuals, and moderate to strong neutralizing immunity induced against BA.2 in Delta and BA.1 breakthrough infections.
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Affiliation(s)
- Noah Brazer
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Mary Kate Morris
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Khamal Anglin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Prachi Saldhi
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Miguel Garcia-Knight
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Sutana Bethancourt
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | | | - Baolin Wang
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Abiodun Foresythe
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jenny Nguyen
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Amelia S Gliwa
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jesus Pineda-Ramirez
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Ruth Diaz Sanchez
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Yueyuan Zhang
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Melanie Ott
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
- Gladstone Institutes, San Francisco, CA, USA
- Innovative Genomics Institute, University of California Berkeley, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Debra A Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - J Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Carl Hanson
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Charles Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California Berkeley, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
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