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Selvavinayagam ST, Sankar S, Yong YK, Murugesan A, Suvaithenamudhan S, Hemashree K, Rajeshkumar M, Kumaresan A, Pandey RP, Shanmugam S, Arthydevi P, Kumar MS, Gopalan N, Kannan M, Cheedarla N, Tan HY, Zhang Y, Larsson M, Balakrishnan P, Velu V, Byrareddy SN, Shankar EM, Raju S. Emergence of SARS-CoV-2 Omicron Variant JN.1 in Tamil Nadu, India - Clinical Characteristics and Novel Mutations. medRxiv 2024:2024.04.16.24305882. [PMID: 38699322 PMCID: PMC11065016 DOI: 10.1101/2024.04.16.24305882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
In December 2023, we observed a notable shift in the COVID-19 landscape, when the JN.1 emerged as a predominant SARS-CoV-2 variant with a 95% incidence. We characterized the clinical profile, and genetic changes in JN.1, an emerging SARS-CoV-2 variant of interest. Whole genome sequencing was performed on SARS-CoV-2 positive samples, followed by sequence analysis. Mutations within the spike protein sequences were analyzed and compared with the previous lineages and sublineages of SARS-CoV-2, to identify the potential impact of these unique mutations on protein structure and possible functionality. Several unique and dynamic mutations were identified herein. Our data provides key insights into the emergence of newer variants of SARS-CoV-2 in our region and highlights the need for robust and sustained genomic surveillance of SARS-CoV-2.
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Selvavinayagam ST, Suvaithenamudhan S, Yong YK, Hemashree K, Rajeshkumar M, Kumaresan A, Arthydevi P, Kannan M, Gopalan N, Vignesh R, Murugesan A, Sivasankaran MP, Sankar S, Cheedarla N, Anshad AR, Govindaraj S, Zhang Y, Tan HY, Larsson M, Saravanan S, Balakrishnan P, Kulanthaivel L, Singh K, Joseph N, Velu V, Byrareddy SN, Shankar EM, Raju S. Genomic surveillance of omicron B.1.1.529 SARS-CoV-2 and its variants between December 2021 and March 2023 in Tamil Nadu, India-A state-wide prospective longitudinal study. J Med Virol 2024; 96:e29456. [PMID: 38329187 DOI: 10.1002/jmv.29456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/10/2024] [Accepted: 01/23/2024] [Indexed: 02/09/2024]
Abstract
A state-wide prospective longitudinal investigation of the genomic surveillance of the omicron B.1.1.529 SARS-CoV-2 variant and its sublineages in Tamil Nadu, India, was conducted between December 2021 and March 2023. The study aimed to elucidate their mutational patterns and their genetic interrelationship in the Indian population. The study identified several unique mutations at different time-points, which likely could attribute to the changing disease characteristics, transmission, and pathogenicity attributes of omicron variants. The study found that the omicron variant is highly competent in its mutating potentials, and that it continues to evolve in the general population, likely escaping from natural as well as vaccine-induced immune responses. Our findings suggest that continuous surveillance of viral variants at the global scenario is warranted to undertake intervention measures against potentially precarious SARS-CoV-2 variants and their evolution.
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Affiliation(s)
- Sivaprakasam T Selvavinayagam
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu, India
| | - Suvaiyarasan Suvaithenamudhan
- Infection and Inflammation, Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India
- School of Biomedical Sciences, Sri Balaji Vidyapeeth, (Deemed to be University), Pondicherry, India
| | - Yean K Yong
- Laboratory Centre, Xiamen University Malaysia, Sepang, Selangor, Malaysia
- Kelip-kelip! Center of Excellence for Light Enabling Technologies, Xiamen University Malaysia, Sepang, Selangor, Malaysia
| | - Kannan Hemashree
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu, India
| | - Manivannan Rajeshkumar
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu, India
| | - Anandhazhvar Kumaresan
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu, India
| | - Parthiban Arthydevi
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu, India
| | - Meganathan Kannan
- Blood and Vascular Biology, Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India
| | - Natarajan Gopalan
- Department of Epidemiology and Public Health, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India
| | - Ramachandran Vignesh
- Preclinical Department, Faculty of Medicine, Royal College of Medicine Perak, Universiti Kuala Lumpur, Ipoh, Perak, Malaysia
| | - Amudhan Murugesan
- Department of Microbiology, The Government Theni Medical College and Hospital, Theni, Tamil Nadu, India
| | | | - Sathish Sankar
- Department of Microbiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Science, Chennai, Tamil Nadu, India
| | - Narayanaiah Cheedarla
- Division of Microbiology and Immunology, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Emory National Primate Research Center, Emory Vaccine Center, Atlanta, Georgia, USA
| | - Abdul R Anshad
- Infection and Inflammation, Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India
| | - Sakthivel Govindaraj
- Division of Microbiology and Immunology, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Emory National Primate Research Center, Emory Vaccine Center, Atlanta, Georgia, USA
| | - Ying Zhang
- Kelip-kelip! Center of Excellence for Light Enabling Technologies, Xiamen University Malaysia, Sepang, Selangor, Malaysia
- Chemical Engineering, Xiamen University Malaysia, Sepang, Malaysia
| | - Hong Y Tan
- Laboratory Centre, Xiamen University Malaysia, Sepang, Selangor, Malaysia
- School of Traditional Chinese Medicine, Xiamen University Malaysia, Sepang, Malaysia
| | - Marie Larsson
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Shanmugam Saravanan
- Center for Infectious Diseases, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu, India
| | - Pachamuthu Balakrishnan
- Center for Infectious Diseases, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu, India
| | - Langeswaran Kulanthaivel
- Department of Biomedical Science, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Kamalendra Singh
- Bond Life Sciences Center, Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, USA
| | - Narcisse Joseph
- Department of Medical Microbiology, Universiti Putra Malaysia, Kuala Lumpur, Malaysia
| | - Vijayakumar Velu
- Division of Microbiology and Immunology, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Emory National Primate Research Center, Emory Vaccine Center, Atlanta, Georgia, USA
| | - Siddappa N Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Esaki M Shankar
- Infection and Inflammation, Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India
| | - Sivadoss Raju
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu, India
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Cheedarla N, Verkerke HP, Potlapalli S, McLendon KB, Patel A, Frank F, O’Sick WH, Cheedarla S, Baugh TJ, Damhorst GL, Wu H, Graciaa D, Hudaib F, Alter DN, Bryksin J, Ortlund EA, Guarner J, Auld S, Shah S, Lam W, Mattoon D, Johnson JM, Wilson DH, Dhodapkar MV, Stowell SR, Neish AS, Roback JD. Rapid, high throughput, automated detection of SARS-CoV-2 neutralizing antibodies against Wuhan-WT, delta and omicron BA1, BA2 spike trimers. iScience 2023; 26:108256. [PMID: 37965140 PMCID: PMC10641509 DOI: 10.1016/j.isci.2023.108256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 05/17/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Traditional cellular and live-virus methods for detection of SARS-CoV-2 neutralizing antibodies (nAbs) are labor- and time-intensive, and thus not suited for routine use in the clinical lab to predict vaccine efficacy and natural immune protection. Here, we report the development and validation of a rapid, high throughput method for measuring SARS-CoV-2 nAbs against native-like trimeric spike proteins. This assay uses a blockade of human angiotensin converting enzyme 2 (hACE-2) binding (BoAb) approach in an automated digital immunoassay on the Quanterix HD-X platform. BoAb assays using Wuhan-WT (vaccine strain), delta (B.1.167.2), omicron BA1 and BA2 variant viral strains showed strong correlation with cell-based pseudovirus neutralization activity (PNA) and live-virus neutralization activity. Importantly, we were able to detect similar patterns of delta and omicron variant resistance to neutralization in samples with paired vaccine strain and delta variant BoAb measurements. Finally, we screened clinical samples from patients with or without evidence of SARS-CoV-2 exposure by a single-dilution screening version of our assays, finding significant nAb activity only in exposed individuals. Importantly, this completely automated assay can be performed in 4 h to measure neutralizing antibody titers for 16 samples over 8 serial dilutions or, 128 samples at a single dilution with replicates. In principle, these assays offer a rapid, robust, and scalable alternative to time-, skill-, and cost-intensive standard methods for measuring SARS-CoV-2 nAb levels.
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Affiliation(s)
- Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hans P. Verkerke
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Sindhu Potlapalli
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kaleb Benjamin McLendon
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anamika Patel
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Filipp Frank
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - William Henry O’Sick
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Suneethamma Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Tyler Jon Baugh
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Gregory L. Damhorst
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, GA 30322, USA
| | - Huixia Wu
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Daniel Graciaa
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, GA 30322, USA
| | - Fuad Hudaib
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - David N. Alter
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Janetta Bryksin
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Eric A. Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jeanette Guarner
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sara Auld
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, GA 30322, USA
| | - Sarita Shah
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, GA 30322, USA
- Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Wilbur Lam
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Dawn Mattoon
- Quanterix Corporation, 900 Middlesex Turnpike, Billerica, MA 01821, USA
| | - Joseph M. Johnson
- Quanterix Corporation, 900 Middlesex Turnpike, Billerica, MA 01821, USA
| | - David H. Wilson
- Quanterix Corporation, 900 Middlesex Turnpike, Billerica, MA 01821, USA
| | - Madhav V. Dhodapkar
- Department of Hematology/Medical Oncology, Emory University, Atlanta, GA, USA
| | - Sean R. Stowell
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Andrew S. Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John D. Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
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Forrest AD, Poliektov NE, Easley KA, Michopoulos V, Ravi M, Cheedarla N, Neish AS, Cheedarla S, Roback JD, Dunlop AL, Badell ML, Dude CM. Characterization of the inflammatory response to COVID-19 illness in pregnancy. Cytokine 2023; 170:156319. [PMID: 37544133 DOI: 10.1016/j.cyto.2023.156319] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/08/2023]
Abstract
OBJECTIVE Pregnant patients face greater morbidity and mortality from COVID-19 related illness than their non-pregnant peers. Previous research in non-pregnant patients established that poor clinical outcomes in SARS-CoV-2 positive patients admitted to the ICU were correlated with a significant increase in the proinflammatory markers interleukin (IL)-1β, IL-6, IL-8, and IL-10. Importantly, high levels of these inflammatory markers have also been associated with adverse pregnancy outcomes, including spontaneous preterm birth, preeclampsia, and severe respiratory disease. STUDY DESIGN This was a retrospective cohort study that compared the serum inflammatory cytokine profiles of pregnant patients with acute/post-acute SARS-CoV-2 infection to those with previous exposure. All subjects in both cohorts tested positive for SARS-CoV-2 antibodies; however, those in the acute/post-acute infection cohort had a documented positive SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) result within 30 days of serum sample collection. Serum samples were obtained during prenatal venipuncture from 13 to 39 weeks' gestation and the cohorts were matched by gestational age. The inflammatory cytokines interferon (IFN)-γ, IL-10, IL-1β, IL-4, IL-6, IL-8, and tumor necrosis factor (TNF)-α were assayed from maternal serum using a standard ELISA assay and median cytokine concentrations were compared using the Mann-Whitney test. RESULTS AND DISCUSSION We enrolled 50 non-Hispanic Black patients with confirmed COVID-19 infection who received prenatal care at Grady Memorial Hospital in Atlanta, Georgia. Those with acute/post-acute infection (n = 22) had significantly higher concentrations of SARS-CoV-2 antibody, IL-10, IL-1β, and IL-8, while patients with previous exposure (n = 28) had significantly higher concentrations of IL-4. There were no significant inter-group differences in medical comorbidities. Pregnant patients with acute/post-acute SARS-CoV-2 infection had significantly higher serum concentrations of pro-inflammatory cytokines as compared to those with previous exposure, suggesting that, like in the non-pregnant population, SARS-CoV-2 infection alters the levels of circulating proinflammatory markers during pregnancy. The increased levels of cytokines may contribute to the adverse obstetric outcomes observed with COVID-19 illness.
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Affiliation(s)
- Alexandra D Forrest
- Johns Hopkins University, Department of Gynecology and Obstetrics, Baltimore, MD, United States.
| | - Natalie E Poliektov
- Johns Hopkins University, Department of Gynecology and Obstetrics, Baltimore, MD, United States
| | - Kirk A Easley
- Emory University Rollins School of Public Health, Department of Biostatistics and Bioinformatics, Atlanta, GA, United States
| | - Vasiliki Michopoulos
- Emory University School of Medicine, Department of Psychiatry and Behavioral Sciences, Atlanta, GA, United States
| | - Meghna Ravi
- Emory University School of Medicine, Department of Psychiatry and Behavioral Sciences, Atlanta, GA, United States
| | - Narayanaiah Cheedarla
- Emory University School of Medicine, Department of Pathology and Laboratory Medicine, Atlanta, GA, United States
| | - Andrew S Neish
- Emory University School of Medicine, Department of Pathology and Laboratory Medicine, Atlanta, GA, United States
| | - Suneetha Cheedarla
- Emory University School of Medicine, Department of Pathology and Laboratory Medicine, Atlanta, GA, United States
| | - John D Roback
- Emory University School of Medicine, Department of Pathology and Laboratory Medicine, Atlanta, GA, United States
| | - Anne L Dunlop
- Johns Hopkins University, Department of Gynecology and Obstetrics, Baltimore, MD, United States
| | - Martina L Badell
- Johns Hopkins University, Department of Gynecology and Obstetrics, Baltimore, MD, United States
| | - Carolynn M Dude
- Johns Hopkins University, Department of Gynecology and Obstetrics, Baltimore, MD, United States
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5
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Patel A, Kumar S, Lai L, Keen M, Valanparambil R, Chakravarthy C, Laughlin Z, Frank F, Cheedarla N, Verkerke HP, Neish AS, Roback JD, Davis CW, Wrammert J, Sharma A, Ahmed R, Suthar MS, Murali-Krishna K, Chandele A, Ortlund E. Light chain of a public SARS-CoV-2 class-3 antibody modulates neutralization against Omicron. Cell Rep 2023; 42:113150. [PMID: 37708028 PMCID: PMC10862350 DOI: 10.1016/j.celrep.2023.113150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/14/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023] Open
Abstract
The pairing of antibody genes IGHV2-5/IGLV2-14 is established as a public immune response that potently cross-neutralizes SARS-CoV-2 variants, including Omicron, by targeting class-3/RBD-5 epitopes in the receptor binding domain (RBD). LY-CoV1404 (bebtelovimab) exemplifies this, displaying exceptional potency against Omicron sub-variants up to BA.5. Here, we report a human antibody, 002-S21B10, encoded by the public clonotype IGHV2-5/IGLV2-14. While 002-S21B10 neutralized key SARS-CoV-2 variants, it did not neutralize Omicron, despite sharing >92% sequence similarity with LY-CoV1404. The structure of 002-S21B10 in complex with spike trimer plus structural and sequence comparisons with LY-CoV1404 and other IGHV2-5/IGLV2-14 antibodies revealed significant variations in light-chain orientation, paratope residues, and epitope-paratope interactions that enable some antibodies to neutralize Omicron but not others. Confirming this, replacing the light chain of 002-S21B10 with the light chain of LY-CoV1404 restored 002-S21B10's binding to Omicron. Understanding such Omicron evasion from public response is vital for guiding therapeutics and vaccine design.
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Affiliation(s)
- Anamika Patel
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sanjeev Kumar
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India; Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Lilin Lai
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Meredith Keen
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Rajesh Valanparambil
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Chennareddy Chakravarthy
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Zane Laughlin
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Filipp Frank
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hans P Verkerke
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Andrew S Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John D Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Carl W Davis
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Jens Wrammert
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Amit Sharma
- Structural Parasitology Group, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Rafi Ahmed
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Mehul S Suthar
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Kaja Murali-Krishna
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India; Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA.
| | - Anmol Chandele
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India.
| | - Eric Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.
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6
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Nakahara H, Cheedarla N, Verkerke HP, Cheedarla S, Wu SC, Hendrickson JE, Chang A, McLemore ML, El Rassi F, Roback JD, Neish AS, Fasano RM, Stowell SR. Enhanced IgG immune response to COVID-19 vaccination in patients with sickle cell disease. Br J Haematol 2023; 202:937-941. [PMID: 37287128 PMCID: PMC10751105 DOI: 10.1111/bjh.18899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/09/2023]
Abstract
Patients with sickle cell disease (SCD) are considered to be immunocompromised, yet data on the antibody response to SARS-CoV-2 vaccination in SCD is limited. We investigated anti-SARS-CoV-2 IgG titres and overall neutralizing activity in 201 adults with SCD and demographically matched non-SCD controls. Unexpectedly, patients with SCD generate a more robust and durable COVID-19 vaccine IgG response compared to matched controls, though the neutralizing activity remained similar across both cohorts. These findings suggest that patients with SCD achieve a similar antibody response following COVID-19 vaccination compared to the general population, with implications for optimal vaccination strategies for patients with SCD.
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Affiliation(s)
- Hirotomo Nakahara
- Center for Transfusion Medicine and Cellular Therapies, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Hans P Verkerke
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Suneethamma Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Shang-Chuen Wu
- Joint Program in Transfusion Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeanne E Hendrickson
- Center for Transfusion Medicine and Cellular Therapies, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Andres Chang
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Morgan L McLemore
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Fuad El Rassi
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, USA
| | - John D Roback
- Center for Transfusion Medicine and Cellular Therapies, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Andrew S Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ross M Fasano
- Center for Transfusion Medicine and Cellular Therapies, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Sean R Stowell
- Joint Program in Transfusion Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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7
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Wu SC, Arthur CM, Jan HM, Garcia-Beltran WF, Patel KR, Rathgeber MF, Verkerke HP, Cheedarla N, Jajosky RP, Paul A, Neish AS, Roback JD, Josephson CD, Wesemann DR, Kalman D, Rakoff-Nahoum S, Cummings RD, Stowell SR. Blood group A enhances SARS-CoV-2 infection. Blood 2023; 142:742-747. [PMID: 37367252 PMCID: PMC10294591 DOI: 10.1182/blood.2022018903] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/18/2023] [Accepted: 05/02/2023] [Indexed: 06/28/2023] Open
Abstract
Among the risk factors for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), ABO(H) blood group antigens are among the most recognized predictors of infection. However, the mechanisms by which ABO(H) antigens influence susceptibility to COVID-19 remain incompletely understood. The receptor-binding domain (RBD) of SARS-CoV-2, which facilitates host cell engagement, bears significant similarity to galectins, an ancient family of carbohydrate-binding proteins. Because ABO(H) blood group antigens are carbohydrates, we compared the glycan-binding specificity of SARS-CoV-2 RBD with that of galectins. Similar to the binding profile of several galectins, the RBDs of SARS-CoV-2, including Delta and Omicron variants, exhibited specificity for blood group A. Not only did each RBD recognize blood group A in a glycan array format, but each SARS-CoV-2 virus also displayed a preferential ability to infect blood group A-expressing cells. Preincubation of blood group A cells with a blood group-binding galectin specifically inhibited the blood group A enhancement of SARS-CoV-2 infection, whereas similar incubation with a galectin that does not recognize blood group antigens failed to impact SARS-CoV-2 infection. These results demonstrated that SARS-CoV-2 can engage blood group A, providing a direct link between ABO(H) blood group expression and SARS-CoV-2 infection.
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Affiliation(s)
- Shang-Chuen Wu
- Department of Pathology, Joint Program in Transfusion Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Connie M Arthur
- Department of Pathology, Joint Program in Transfusion Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Hau-Ming Jan
- Department of Pathology, Joint Program in Transfusion Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Wilfredo F Garcia-Beltran
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA
| | - Kashyap R Patel
- Department of Pathology, Joint Program in Transfusion Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Matthew F Rathgeber
- Department of Pathology, Joint Program in Transfusion Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Hans P Verkerke
- Department of Pathology, Joint Program in Transfusion Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA
| | - Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA
| | - Ryan Philip Jajosky
- Department of Pathology, Joint Program in Transfusion Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Anu Paul
- Department of Pathology, Joint Program in Transfusion Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Andrew S Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA
| | - John D Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA
- Center for Transfusion Medicine and Cellular Therapies, Emory University School of Medicine, Atlanta, GA
| | - Cassandra D Josephson
- Department of Hematology and Oncology, Johns Hopkins University All Children's Hospital, St. Petersburg, FL
| | - Duane R Wesemann
- Division of Allergy and Clinical Immunology and Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Daniel Kalman
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA
| | - Seth Rakoff-Nahoum
- Division of Infectious Disease, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Richard D Cummings
- National Center for Functional Glycomics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Sean R Stowell
- Department of Pathology, Joint Program in Transfusion Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
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Patel A, Kumar S, Lai L, Chakravarthy C, Valanparambil R, Reddy ES, Gottimukkala K, Bajpai P, Raju DR, Edara VV, Davis-Gardner ME, Linderman S, Dixit K, Sharma P, Mantus G, Cheedarla N, Verkerke HP, Frank F, Neish AS, Roback JD, Davis CW, Wrammert J, Ahmed R, Suthar MS, Sharma A, Murali-Krishna K, Chandele A, Ortlund EA. Molecular basis of SARS-CoV-2 Omicron variant evasion from shared neutralizing antibody response. Structure 2023; 31:801-811.e5. [PMID: 37167972 PMCID: PMC10171968 DOI: 10.1016/j.str.2023.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/09/2023] [Accepted: 04/21/2023] [Indexed: 05/13/2023]
Abstract
Understanding the molecular features of neutralizing epitopes is important for developing vaccines/therapeutics against emerging SARS-CoV-2 variants. We describe three monoclonal antibodies (mAbs) generated from COVID-19 recovered individuals during the first wave of the pandemic in India. These mAbs had publicly shared near germline gene usage and potently neutralized Alpha and Delta, poorly neutralized Beta, and failed to neutralize Omicron BA.1 SARS-CoV-2 variants. Structural analysis of these mAbs in complex with trimeric spike protein showed that all three mAbs bivalently bind spike with two mAbs targeting class 1 and one targeting a class 4 receptor binding domain epitope. The immunogenetic makeup, structure, and function of these mAbs revealed specific molecular interactions associated with the potent multi-variant binding/neutralization efficacy. This knowledge shows how mutational combinations can affect the binding or neutralization of an antibody, which in turn relates to the efficacy of immune responses to emerging SARS-CoV-2 escape variants.
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Affiliation(s)
- Anamika Patel
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sanjeev Kumar
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Lilin Lai
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Chennareddy Chakravarthy
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Rajesh Valanparambil
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Elluri Seetharami Reddy
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India; Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi 110016, India
| | - Kamalvishnu Gottimukkala
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Prashant Bajpai
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Dinesh Ravindra Raju
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA; Georgia Tech, Atlanta, GA 30332, USA
| | - Venkata Viswanadh Edara
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Meredith E Davis-Gardner
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Susanne Linderman
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Kritika Dixit
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Pragati Sharma
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Grace Mantus
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hans P Verkerke
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Filipp Frank
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andrew S Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John D Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Carl W Davis
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Jens Wrammert
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Rafi Ahmed
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Mehul S Suthar
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Amit Sharma
- Structural Parasitology Group, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India.
| | - Kaja Murali-Krishna
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India; Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA.
| | - Anmol Chandele
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India.
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.
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Govindaraj S, Cheedarla N, Cheedarla S, Irby LS, Neish AS, Roback JD, Smith AK, Velu V. COVID-19 vaccine induced poor neutralization titers for SARS-CoV-2 omicron variants in maternal and cord blood. Front Immunol 2023; 14:1211558. [PMID: 37465682 PMCID: PMC10350671 DOI: 10.3389/fimmu.2023.1211558] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/12/2023] [Indexed: 07/20/2023] Open
Abstract
Introduction Maternally derived antibodies are crucial for neonatal immunity. Understanding the binding and cross-neutralization capacity of maternal and cord antibody responses to SARS-CoV-2 variants following COVID-19 vaccination in pregnancy can inform neonatal immunity. Methods Here we characterized the binding and neutralizing antibody profile at delivery in 24 pregnant individuals following two doses of Moderna mRNA-1273 or Pfizer BNT162b2 vaccination. We analyzed for SARS-CoV-2 multivariant cross-neutralizing antibody levels for wildtype Wuhan, Delta, Omicron BA1, BA2, and BA4/BA5 variants. In addition, we evaluated the transplacental antibody transfer by profiling maternal and umbilical cord blood. Results Our results reveal that the current COVID-19 vaccination induced significantly higher RBD-specific binding IgG titers in cord blood compared to maternal blood for both the Wuhan and Omicron BA1 strain. Interestingly, the binding IgG antibody levels for the Omicron BA1 strain were significantly lower when compared to the Wuhan strain in both maternal and cord blood. In contrast to the binding, the Omicron BA1, BA2, and BA4/5 specific neutralizing antibody levels were significantly lower compared to the Wuhan and Delta variants. It is interesting to note that the BA4/5 neutralizing capacity was not detected in either maternal or cord blood. Discussion Our data suggest that the initial series of COVID-19 mRNA vaccines were immunogenic in pregnant women, and vaccine-elicited binding antibodies were detectable in cord blood at significantly higher levels for the Wuhan and Delta variants but not for the Omicron variants. Interestingly, the vaccination did not induce neutralizing antibodies for Omicron variants. These results provide novel insight into the impact of vaccination on maternal humoral immune response and transplacental antibody transfer for SARS-CoV-2 variants and support the need for bivalent boosters as new variants emerge.
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Affiliation(s)
- Sakthivel Govindaraj
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
- Division of Microbiology and Immunology, Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Suneethamma Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - LesShon S. Irby
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, United States
| | - Andrew S. Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - John D. Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Alicia K. Smith
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, United States
| | - Vijayakumar Velu
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
- Division of Microbiology and Immunology, Emory Vaccine Center, Emory University, Atlanta, GA, United States
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10
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Faliti CE, Anam FA, Cheedarla N, Woodruff MC, Usman SY, Runnstrom MC, Van TT, Kyu S, Ahmed H, Morrison-Porter A, Quehl H, Haddad NS, Chen W, Cheedarla S, Neish AS, Roback JD, Antia R, Khosroshahi A, Lee FEH, Sanz I. Poor immunogenicity upon SARS-CoV-2 mRNA vaccinations in autoimmune SLE patients is associated with pronounced EF-mediated responses and anti-BAFF/Belimumab treatment. medRxiv 2023:2023.06.08.23291159. [PMID: 37398319 PMCID: PMC10312827 DOI: 10.1101/2023.06.08.23291159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Novel mRNA vaccines have resulted in a reduced number of SARS-CoV-2 infections and hospitalizations. Yet, there is a paucity of studies regarding their effectiveness on immunocompromised autoimmune subjects. In this study, we enrolled subjects naïve to SARS-CoV-2 infections from two cohorts of healthy donors (HD, n=56) and systemic lupus erythematosus (SLE, n=69). Serological assessments of their circulating antibodies revealed a significant reduction of potency and breadth of neutralization in the SLE group, only partially rescued by a 3rd booster dose. Immunological memory responses in the SLE cohort were characterized by a reduced magnitude of spike-reactive B and T cell responses that were strongly associated with poor seroconversion. Vaccinated SLE subjects were defined by a distinct expansion and persistence of a DN2 spike-reactive memory B cell pool and a contraction of spike-specific memory cTfh cells, contrasting with the sustained germinal center (GC)-driven activity mediated by mRNA vaccination in the healthy population. Among the SLE-associated factors that dampened the vaccine responses, treatment with the monoclonal antibody anti-BAFF/Belimumab (a lupus FDA-approved B cell targeting agent) profoundly affected the vaccine responsiveness by restricting the de novo B cell responses and promoting stronger extra-follicular (EF)-mediated responses that were associated with poor immunogenicity and impaired immunological memory. In summary, this study interrogates antigen-specific responses and characterized the immune cell landscape associated with mRNA vaccination in SLE. The identification of factors associated with reduced vaccine efficacy illustrates the impact of SLE B cell biology on mRNA vaccine responses and provides guidance for the management of boosters and recall vaccinations in SLE patients according to their disease endotype and modality of treatment.
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Affiliation(s)
- Caterina E. Faliti
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - Fabliha A. Anam
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Matthew C. Woodruff
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - Sabeena Y. Usman
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - Martin C. Runnstrom
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University, Atlanta, GA, USA
| | - Trinh T.P. Van
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - Shuya Kyu
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University, Atlanta, GA, USA
| | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Andrea Morrison-Porter
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hannah Quehl
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University, Atlanta, GA, USA
| | - Natalie S. Haddad
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University, Atlanta, GA, USA
- MicroB-plex, Atlanta, GA, USA
| | | | - Suneethamma Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andrew S. Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John D. Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Arezou Khosroshahi
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - F. Eun-Hyung Lee
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University, Atlanta, GA, USA
| | - Ignacio Sanz
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
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11
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Damhorst GL, Schoof N, Nguyen PV, Verkerke H, Wilber E, McLendon K, O’Sick W, Baugh T, Cheedarla S, Cheedarla N, Stittleburg V, Fitts EC, Neja MA, Babiker A, Piantadosi A, Roback JD, Waggoner JJ, Mavigner M, Lam WA. Investigation of Blood Plasma Viral Nucleocapsid Antigen as a Marker of Active Severe Acute Respiratory Syndrome Coronavirus 2 Omicron Variant Infection. Open Forum Infect Dis 2023; 10:ofad226. [PMID: 37213426 PMCID: PMC10199120 DOI: 10.1093/ofid/ofad226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/26/2023] [Indexed: 05/23/2023] Open
Abstract
Background Nasopharyngeal qualitative reverse-transcription polymerase chain reaction (RT-PCR) is the gold standard for diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but it is not practical or sufficient in every clinical scenario due to its inability to distinguish active from resolved infection. Alternative or adjunct testing may be needed to guide isolation precautions and treatment in patients admitted to the hospital. Methods We performed a single-center, retrospective analysis of residual clinical specimens and medical record data to examine blood plasma nucleocapsid antigen as a candidate biomarker of active SARS-CoV-2. Adult patients admitted to the hospital or presenting to the emergency department with SARS-CoV-2 ribonucleic acid (RNA) detected by RT-PCR from a nasopharyngeal swab specimen were included. Both nasopharyngeal swab and a paired whole blood sample were required to be available for analysis. Results Fifty-four patients were included. Eight patients had positive nasopharyngeal swab virus cultures, 7 of whom (87.5%) had concurrent antigenemia. Nineteen (79.2%) of 24 patients with detectable subgenomic RNA and 20 (80.0%) of 25 patients with N2 RT-PCR cycle threshold ≤ 33 had antigenemia. Conclusions Most individuals with active SARS-CoV-2 infection are likely to have concurrent antigenemia, but there may be some individuals with active infection in whom antigenemia is not detectable. The potential for high sensitivity and convenience of a blood test prompts interest in further investigation as a screening tool to reduce reliance on nasopharyngeal swab sampling and as an adjunct diagnostic test to aid in clinical decision making during the period after acute coronavirus disease 2019.
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Affiliation(s)
- Gregory L Damhorst
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
| | - Nils Schoof
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Phuong-Vi Nguyen
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Hans Verkerke
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
| | - Eli Wilber
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Kaleb McLendon
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
| | - William O’Sick
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
| | - Tyler Baugh
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
| | - Suneethamma Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
| | - Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
| | - Victoria Stittleburg
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Eric C Fitts
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
| | - Margaret A Neja
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ahmed Babiker
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
| | - Anne Piantadosi
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
| | - John D Roback
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
| | - Jesse J Waggoner
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Maud Mavigner
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Wilbur A Lam
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Aflac Cancer and Blood Disorders Center at Children's Healthcare of Atlanta, Atlanta, Georgia, USA
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
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12
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Chaubey I, Vijay H, Govindaraj S, Babu H, Cheedarla N, Shankar EM, Vignesh R, Velu V. Impact of COVID-19 Vaccination on Pregnant Women. Pathogens 2023; 12:431. [PMID: 36986353 PMCID: PMC10056326 DOI: 10.3390/pathogens12030431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/16/2023] [Accepted: 03/07/2023] [Indexed: 03/11/2023] Open
Abstract
In light of the COVID-19 pandemic, researchers across the world hastened to develop vaccines that would aid in bolstering herd immunity. Utilizing mRNA coding and viral vector technology, the currently approved vaccines were required to undergo extensive testing to confirm their safety for mass usage in the general population. However, clinical trials failed to test the safety and efficacy of the COVID-19 vaccines in groups with weakened immune systems, especially pregnant women. Lack of information on the effects of vaccinations in pregnancy and the safety of fetuses are among the topmost reasons preventing pregnant women from receiving immunization. Thus, the lack of data examining the effects of COVID-19 vaccinations on pregnant women must be addressed. This review focused on the safety and efficacy of the approved COVID-19 vaccinations in pregnancy and their impact on both maternal and fetal immune responses. For that, we took the approach of combined systematic review/meta-analysis and compiled the available data from the original literature from PubMed, Web of Science, EMBASE and Medline databases. All articles analyzed presented no adverse effects of vaccination in pregnancy, with varying conclusions on the degree of effectiveness. The majority of the findings described robust immune responses in vaccinated pregnant women, successful transplacental antibody transfer, and implications for neonatal immunity. Hence, findings from the cumulative data available can be helpful in achieving COVID-19 herd immunization, including pregnant women.
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Affiliation(s)
- Ishaan Chaubey
- Molecular and Cellular Biology, Department of Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Harini Vijay
- College of Arts and Sciences, University of Washington, Seattle, WA 98195, USA
| | - Sakthivel Govindaraj
- Division of Microbiology and Immunology, Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
- Laboratory Medicine, Department of Pathology, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Hemalatha Babu
- Division of Microbiology and Immunology, Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
- Laboratory Medicine, Department of Pathology, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Narayanaiah Cheedarla
- Laboratory Medicine, Department of Pathology, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Esaki M. Shankar
- Infection and Inflammation, Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur 610005, India
| | - Ramachandran Vignesh
- Preclinical Department, Faculty of Medicine, Royal College of Medicine Perak, Universiti Kuala Lumpur, Ipoh 30405, Malaysia
| | - Vijayakumar Velu
- Division of Microbiology and Immunology, Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
- Laboratory Medicine, Department of Pathology, School of Medicine, Emory University, Atlanta, GA 30322, USA
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13
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Azeem MI, Nooka AK, Shanmugasundaram U, Cheedarla N, Potdar S, Manalo RJ, Moreno A, Switchenko JM, Cheedarla S, Doxie DB, Radzievski R, Ellis ML, Manning KE, Wali B, Valanparambil RM, Maples KT, Baymon E, Kaufman JL, Hofmeister CC, Joseph NS, Lonial S, Roback JD, Sette A, Ahmed R, Suthar MS, Neish AS, Dhodapkar MV, Dhodapkar KM. Impaired SARS-CoV-2 Variant Neutralization and CD8+ T-cell Responses Following 3 Doses of mRNA Vaccines in Myeloma: Correlation with Breakthrough Infections. Blood Cancer Discov 2023; 4:106-117. [PMID: 36511813 PMCID: PMC9975771 DOI: 10.1158/2643-3230.bcd-22-0173] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/23/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
Patients with multiple myeloma (MM) mount suboptimal neutralizing antibodies (nAb) following 2 doses of SARS-CoV-2 mRNA vaccines. Currently, circulating SARS-CoV-2 variants of concern (VOC) carry the risk of breakthrough infections. We evaluated immune recognition of current VOC including BA.1, BA.2, and BA.5 in 331 racially representative patients with MM following 2 or 3 doses of mRNA vaccines. The third dose increased nAbs against WA1 in 82%, but against BA variants in only 33% to 44% of patients. Vaccine-induced nAbs correlated with receptor-binding domain (RBD)-specific class-switched memory B cells. Vaccine-induced spike-specific T cells were detected in patients without seroconversion and cross-recognized variant-specific peptides but were predominantly CD4+ T cells. Detailed clinical/immunophenotypic analysis identified features correlating with nAb/B/T-cell responses. Patients who developed breakthrough infections following 3 vaccine doses had lower live-virus nAbs, including against VOC. Patients with MM remain susceptible to SARS-CoV-2 variants following 3 vaccine doses and should be prioritized for emerging approaches to elicit variant-nAb and CD8+ T cells. SIGNIFICANCE Three doses of SARS-CoV-2 mRNA vaccines fail to yield detectable VOC nAbs in nearly 60% and spike-specific CD8+ T cells in >80% of myeloma patients. Patients who develop breakthrough infections following vaccination have low levels of live-virus nAb. This article is highlighted in the In This Issue feature, p. 101.
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Affiliation(s)
- Maryam I. Azeem
- Department of Hematology/Medical Oncology, Emory University, Atlanta, Georgia
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University, Atlanta, Georgia
| | - Ajay K. Nooka
- Department of Hematology/Medical Oncology, Emory University, Atlanta, Georgia
- Winship Cancer Institute, Atlanta, Georgia
| | | | | | - Sayalee Potdar
- Department of Hematology/Medical Oncology, Emory University, Atlanta, Georgia
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University, Atlanta, Georgia
| | - Renee Julia Manalo
- Department of Hematology/Medical Oncology, Emory University, Atlanta, Georgia
| | - Alberto Moreno
- Emory Vaccine Center, Emory University, Atlanta, Georgia
- Emory National Primate Research Center, Atlanta, Georgia
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia
| | | | | | | | | | - Madison Leigh Ellis
- Emory Vaccine Center, Emory University, Atlanta, Georgia
- Emory National Primate Research Center, Atlanta, Georgia
| | - Kelly E. Manning
- Emory Vaccine Center, Emory University, Atlanta, Georgia
- Emory National Primate Research Center, Atlanta, Georgia
| | - Bushra Wali
- Emory Vaccine Center, Emory University, Atlanta, Georgia
- Emory National Primate Research Center, Atlanta, Georgia
| | | | | | | | - Jonathan L. Kaufman
- Department of Hematology/Medical Oncology, Emory University, Atlanta, Georgia
- Winship Cancer Institute, Atlanta, Georgia
| | - Craig C. Hofmeister
- Department of Hematology/Medical Oncology, Emory University, Atlanta, Georgia
- Winship Cancer Institute, Atlanta, Georgia
| | - Nisha S. Joseph
- Department of Hematology/Medical Oncology, Emory University, Atlanta, Georgia
- Winship Cancer Institute, Atlanta, Georgia
| | - Sagar Lonial
- Department of Hematology/Medical Oncology, Emory University, Atlanta, Georgia
- Winship Cancer Institute, Atlanta, Georgia
| | - John D. Roback
- Winship Cancer Institute, Atlanta, Georgia
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia
| | | | - Rafi Ahmed
- Winship Cancer Institute, Atlanta, Georgia
- Emory Vaccine Center, Emory University, Atlanta, Georgia
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia
| | - Mehul S. Suthar
- Emory Vaccine Center, Emory University, Atlanta, Georgia
- Emory National Primate Research Center, Atlanta, Georgia
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Andrew S. Neish
- Winship Cancer Institute, Atlanta, Georgia
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia
| | - Madhav V. Dhodapkar
- Department of Hematology/Medical Oncology, Emory University, Atlanta, Georgia
- Winship Cancer Institute, Atlanta, Georgia
| | - Kavita M. Dhodapkar
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University, Atlanta, Georgia
- Winship Cancer Institute, Atlanta, Georgia
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
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14
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Dude CM, Joseph NT, Forrest AD, Verkerke HP, Cheedarla N, Govindaraj S, Irby LS, Easley KA, Smith AK, Stowell SR, Neish A, Amara RR, Jamieson DJ, Dunlop AL, Badell ML, Velu V. Antibody response, neutralizing potency, and transplacental antibody transfer following SARS-CoV-2 infection versus mRNA-1273, BNT162b2 COVID-19 vaccination in pregnancy. Int J Gynaecol Obstet 2023. [PMID: 36598270 DOI: 10.1002/ijgo.14648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 11/16/2022] [Accepted: 12/22/2022] [Indexed: 01/05/2023]
Abstract
OBJECTIVE To improve our understanding of the immune response, including the neutralization antibody response, following COVID-19 vaccination in pregnancy. METHODS This was a prospective cohort study comprising patients with PCR-confirmed SARS-CoV-2 infection and patients who received both doses of mRNA COVID-19 vaccine (mRNA-1273, BNT162b2) in pregnancy recruited from two hospitals in Atlanta, GA, USA. Maternal blood and cord blood at delivery were assayed for anti-receptor binding domain (RBD) IgG, IgA and IgM, and neutralizing antibody. The detection of antibodies, titers, and maternal to fetal transfer ratios were compared. RESULTS Nearly all patients had detectable RBD-binding IgG in maternal and cord samples. The vaccinated versus infected cohort had a significantly greater proportion of cord samples with detectable neutralizing antibody (94% vs. 28%, P < 0.001) and significantly higher transfer ratios for RBD-specific IgG and neutralizing antibodies with a transfer efficiency of 105% (vs. 80%, P < 0.001) and 110% (vs. 90%, P < 0.001), respectively. There was a significant linear decline in maternal and cord blood RBD-specific IgG and neutralizing antibody titers as time from vaccination to delivery increased. CONCLUSIONS Those who receive the mRNA COVID-19 vaccine mount an immune response that is equivalent to-if not greater than-those naturally infected by SARS-CoV-2 during pregnancy.
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Affiliation(s)
- Carolynn M Dude
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Naima T Joseph
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Harvard Medical School Boston, Massachusetts, USA
| | - Alexandra D Forrest
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Hans P Verkerke
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Sakthivel Govindaraj
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA.,Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Les'Shon S Irby
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kirk A Easley
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Alicia K Smith
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Sean R Stowell
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Rama Rao Amara
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA.,Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Denise J Jamieson
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Anne L Dunlop
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Martina L Badell
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Vijayakumar Velu
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA.,Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
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15
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Patel A, Kumar S, Lai L, Chakravarthy C, Valanparambil R, Reddy ES, Gottimukkala K, Bajpai P, Raju DR, Edara VV, Davis-Gardner ME, Linderman S, Dixit K, Sharma P, Mantus G, Cheedarla N, Verkerke HP, Frank F, Neish AS, Roback JD, Davis CW, Wrammert J, Ahmed R, Suthar MS, Sharma A, Murali-Krishna K, Chandele A, Ortlund EA. Molecular basis of SARS-CoV-2 Omicron variant evasion from shared neutralizing antibody response. bioRxiv 2022:2022.10.24.513517. [PMID: 36324804 DOI: 10.1101/2022.10.13.512091] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A detailed understanding of the molecular features of the neutralizing epitopes developed by viral escape mutants is important for predicting and developing vaccines or therapeutic antibodies against continuously emerging SARS-CoV-2 variants. Here, we report three human monoclonal antibodies (mAbs) generated from COVID-19 recovered individuals during first wave of pandemic in India. These mAbs had publicly shared near germline gene usage and potently neutralized Alpha and Delta, but poorly neutralized Beta and completely failed to neutralize Omicron BA.1 SARS-CoV-2 variants. Structural analysis of these three mAbs in complex with trimeric spike protein showed that all three mAbs are involved in bivalent spike binding with two mAbs targeting class-1 and one targeting class-4 Receptor Binding Domain (RBD) epitope. Comparison of immunogenetic makeup, structure, and function of these three mAbs with our recently reported class-3 RBD binding mAb that potently neutralized all SARS-CoV-2 variants revealed precise antibody footprint, specific molecular interactions associated with the most potent multi-variant binding / neutralization efficacy. This knowledge has timely significance for understanding how a combination of certain mutations affect the binding or neutralization of an antibody and thus have implications for predicting structural features of emerging SARS-CoV-2 escape variants and to develop vaccines or therapeutic antibodies against these.
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Affiliation(s)
- Anamika Patel
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sanjeev Kumar
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Lilin Lai
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Chennareddy Chakravarthy
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Rajesh Valanparambil
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Elluri Seetharami Reddy
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, 110016, India
| | - Kamalvishnu Gottimukkala
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Prashant Bajpai
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Dinesh Ravindra Raju
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
- Georgia Tech, Atlanta, GA 30332, USA
| | - Venkata Viswanadh Edara
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Meredith E Davis-Gardner
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Susanne Linderman
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Kritika Dixit
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Pragati Sharma
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Grace Mantus
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hans P Verkerke
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Filipp Frank
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andrew S Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John D Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Carl W Davis
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Jens Wrammert
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Rafi Ahmed
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Mehul S Suthar
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Amit Sharma
- Structural Parasitology Group, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Kaja Murali-Krishna
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Anmol Chandele
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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16
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Patel A, Kumar S, Lai L, Chakravarthy C, Valanparambil R, Reddy ES, Gottimukkala K, Bajpai P, Raju DR, Edara VV, Davis-Gardner ME, Linderman S, Dixit K, Sharma P, Mantus G, Cheedarla N, Verkerke HP, Frank F, Neish AS, Roback JD, Davis CW, Wrammert J, Ahmed R, Suthar MS, Sharma A, Murali-Krishna K, Chandele A, Ortlund EA. Molecular basis of SARS-CoV-2 Omicron variant evasion from shared neutralizing antibody response. bioRxiv 2022:2022.10.24.513517. [PMID: 36324804 PMCID: PMC9628201 DOI: 10.1101/2022.10.24.513517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A detailed understanding of the molecular features of the neutralizing epitopes developed by viral escape mutants is important for predicting and developing vaccines or therapeutic antibodies against continuously emerging SARS-CoV-2 variants. Here, we report three human monoclonal antibodies (mAbs) generated from COVID-19 recovered individuals during first wave of pandemic in India. These mAbs had publicly shared near germline gene usage and potently neutralized Alpha and Delta, but poorly neutralized Beta and completely failed to neutralize Omicron BA.1 SARS-CoV-2 variants. Structural analysis of these three mAbs in complex with trimeric spike protein showed that all three mAbs are involved in bivalent spike binding with two mAbs targeting class-1 and one targeting class-4 Receptor Binding Domain (RBD) epitope. Comparison of immunogenetic makeup, structure, and function of these three mAbs with our recently reported class-3 RBD binding mAb that potently neutralized all SARS-CoV-2 variants revealed precise antibody footprint, specific molecular interactions associated with the most potent multi-variant binding / neutralization efficacy. This knowledge has timely significance for understanding how a combination of certain mutations affect the binding or neutralization of an antibody and thus have implications for predicting structural features of emerging SARS-CoV-2 escape variants and to develop vaccines or therapeutic antibodies against these.
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Affiliation(s)
- Anamika Patel
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sanjeev Kumar
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Lilin Lai
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA,Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Chennareddy Chakravarthy
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA,Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Rajesh Valanparambil
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA,Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Elluri Seetharami Reddy
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India,Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, 110016, India
| | - Kamalvishnu Gottimukkala
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Prashant Bajpai
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Dinesh Ravindra Raju
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Georgia Tech, Atlanta, GA 30332, USA
| | - Venkata Viswanadh Edara
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Meredith E. Davis-Gardner
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Susanne Linderman
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA,Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Kritika Dixit
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Pragati Sharma
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Grace Mantus
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA,Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hans P. Verkerke
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA,Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02215, USA
| | - Filipp Frank
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andrew S. Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John D. Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Carl W. Davis
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA,Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Jens Wrammert
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA,Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Rafi Ahmed
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA,Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Mehul S. Suthar
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA,Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA,Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Amit Sharma
- Structural Parasitology Group, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India,Correspondence: (E.A.O.), (A.C.), (K.M.K.), (A.S.)
| | - Kaja Murali-Krishna
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India,Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA,Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA,Correspondence: (E.A.O.), (A.C.), (K.M.K.), (A.S.)
| | - Anmol Chandele
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India,Correspondence: (E.A.O.), (A.C.), (K.M.K.), (A.S.)
| | - Eric A. Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Correspondence: (E.A.O.), (A.C.), (K.M.K.), (A.S.)
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17
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Kumar S, Patel A, Lai L, Chakravarthy C, Valanparambil R, Reddy ES, Gottimukkala K, Davis-Gardner ME, Edara VV, Linderman S, Nayak K, Dixit K, Sharma P, Bajpai P, Singh V, Frank F, Cheedarla N, Verkerke HP, Neish AS, Roback JD, Mantus G, Goel PK, Rahi M, Davis CW, Wrammert J, Godbole S, Henry AR, Douek DC, Suthar MS, Ahmed R, Ortlund E, Sharma A, Murali-Krishna K, Chandele A. Structural insights for neutralization of Omicron variants BA.1, BA.2, BA.4, and BA.5 by a broadly neutralizing SARS-CoV-2 antibody. Sci Adv 2022; 8:eadd2032. [PMID: 36197988 PMCID: PMC9534492 DOI: 10.1126/sciadv.add2032] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In this study, by characterizing several human monoclonal antibodies (mAbs) isolated from single B cells of the COVID-19–recovered individuals in India who experienced ancestral Wuhan strain (WA.1) of SARS-CoV-2 during early stages of the pandemic, we found a receptor binding domain (RBD)–specific mAb 002-S21F2 that has rare gene usage and potently neutralized live viral isolates of SARS-CoV-2 variants including Alpha, Beta, Gamma, Delta, and Omicron sublineages (BA.1, BA.2, BA.2.12.1, BA.4, and BA.5) with IC
50
ranging from 0.02 to 0.13 μg/ml. Structural studies of 002-S21F2 in complex with spike trimers of Omicron and WA.1 showed that it targets a conformationally conserved epitope on the outer face of RBD (class 3 surface) outside the ACE2-binding motif, thereby providing a mechanistic insights for its broad neutralization activity. The discovery of 002-S21F2 and the broadly neutralizing epitope it targets have timely implications for developing a broad range of therapeutic and vaccine interventions against SARS-CoV-2 variants including Omicron sublineages.
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Affiliation(s)
- Sanjeev Kumar
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi-110 067, India
| | - Anamika Patel
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Lilin Lai
- Department of Pediatrics, Emory University School of Medicine, Emory University Atlanta, GA 30322, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Chennareddy Chakravarthy
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Rajesh Valanparambil
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Elluri Seetharami Reddy
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi-110 067, India
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi-110 016, India
| | - Kamalvishnu Gottimukkala
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi-110 067, India
| | - Meredith E. Davis-Gardner
- Department of Pediatrics, Emory University School of Medicine, Emory University Atlanta, GA 30322, USA
| | - Venkata Viswanadh Edara
- Department of Pediatrics, Emory University School of Medicine, Emory University Atlanta, GA 30322, USA
| | - Susanne Linderman
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Kaustuv Nayak
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi-110 067, India
| | - Kritika Dixit
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi-110 067, India
| | - Pragati Sharma
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi-110 067, India
| | - Prashant Bajpai
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi-110 067, India
| | - Vanshika Singh
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi-110 067, India
| | - Filipp Frank
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hans P. Verkerke
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02215, USA
| | - Andrew S. Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John D. Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Grace Mantus
- Department of Pediatrics, Emory University School of Medicine, Emory University Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Pawan Kumar Goel
- Shaheed Hasan Khan Mewat Government Medical College, Haryana, India
| | - Manju Rahi
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi-110 029, India
| | - Carl W. Davis
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Jens Wrammert
- Department of Pediatrics, Emory University School of Medicine, Emory University Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Sucheta Godbole
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy R. Henry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C. Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mehul S. Suthar
- Department of Pediatrics, Emory University School of Medicine, Emory University Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Rafi Ahmed
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Eric Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Amit Sharma
- ICMR-National Institute of Malaria Research, Dwarka, New Delhi-110 077, India
- Structural Parasitology Group, International Center for Genetic Engineering and Biotechnology, New Delhi-110 067, India
| | - Kaja Murali-Krishna
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi-110 067, India
- Department of Pediatrics, Emory University School of Medicine, Emory University Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Anmol Chandele
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi-110 067, India
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18
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Verkerke HP, Damhorst GL, Graciaa DS, McLendon K, O'Sick W, Robichaux C, Cheedarla N, Potlapalli S, Wu SC, Harrington KRV, Webster A, Kraft C, Rostad CA, Waggoner JJ, Gandhi NR, Guarner J, Auld SC, Neish A, Roback JD, Lam WA, Shah NS, Stowell SR. Nucleocapsid Antigenemia Is a Marker of Acute SARS-CoV-2 Infection. J Infect Dis 2022; 226:1577-1587. [PMID: 35877413 PMCID: PMC9384592 DOI: 10.1093/infdis/jiac225] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/08/2022] [Indexed: 01/07/2023] Open
Abstract
Detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is essential for diagnosis, treatment, and infection control. Polymerase chain reaction (PCR) fails to distinguish acute from resolved infections, as RNA is frequently detected after infectiousness. We hypothesized that nucleocapsid in blood marks acute infection with the potential to enhance isolation and treatment strategies. In a retrospective serosurvey of inpatient and outpatient encounters, we categorized samples along an infection timeline using timing of SARS-CoV-2 testing and symptomatology. Among 1860 specimens from 1607 patients, the highest levels and frequency of antigenemia were observed in samples from acute SARS-CoV-2 infection. Antigenemia was higher in seronegative individuals and in those with severe disease. In our analysis, antigenemia exhibited 85.8% sensitivity and 98.6% specificity as a biomarker for acute coronavirus disease 2019 (COVID-19). Thus, antigenemia sensitively and specifically marks acute SARS-CoV-2 infection. Further study is warranted to determine whether antigenemia may aid individualized assessment of active COVID-19.
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Affiliation(s)
- Hans P Verkerke
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Gregory L Damhorst
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA.,The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
| | - Daniel S Graciaa
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kaleb McLendon
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - William O'Sick
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Sindhu Potlapalli
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Shang Chuen Wu
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kristin R V Harrington
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, Georgia, USA
| | - Andrew Webster
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Colleen Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Christina A Rostad
- Department of Pediatrics and Center for Childhood Infections and Vaccines, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Jesse J Waggoner
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA.,The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA.,Emory Healthcare, Atlanta, Georgia, USA.,Department of Pediatrics and Center for Childhood Infections and Vaccines, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Neel R Gandhi
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA.,Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, Georgia, USA
| | - Jeannette Guarner
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Sara C Auld
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, Georgia, USA.,Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Andrew Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - John D Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Wilbur A Lam
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA.,Department of Pediatrics and Center for Childhood Infections and Vaccines, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia, USA.,Aflac Cancer and Blood Disorders Center at Children's Healthcare of Atlanta, Atlanta, Georgia, USA.,Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - N Sarita Shah
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA.,Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, Georgia, USA
| | - Sean R Stowell
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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19
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Sahoo A, Jones AT, Cheedarla N, Gangadhara S, Roy V, Styles TM, Shiferaw A, Walter KL, Williams LD, Shen X, Ozorowski G, Lee WH, Burton S, Yi L, Song X, Qin ZS, Derdeyn CA, Ward AB, Clements JD, Varadarajan R, Tomaras GD, Kozlowski PA, Alter G, Amara RR. A clade C HIV-1 vaccine protects against heterologous SHIV infection by modulating IgG glycosylation and T helper response in macaques. Sci Immunol 2022; 7:eabl4102. [PMID: 35867800 PMCID: PMC9410801 DOI: 10.1126/sciimmunol.abl4102] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The rising global HIV-1 burden urgently requires vaccines capable of providing heterologous protection. Here, we developed a clade C HIV-1 vaccine consisting of priming with modified vaccinia Ankara (MVA) and boosting with cyclically permuted trimeric gp120 (CycP-gp120) protein, delivered either orally using a needle-free injector or through parenteral injection. We tested protective efficacy of the vaccine against intrarectal challenges with a pathogenic heterologous clade C SHIV infection in rhesus macaques. Both routes of vaccination induced a strong envelope-specific IgG in serum and rectal secretions directed against V1V2 scaffolds from a global panel of viruses with polyfunctional activities. Envelope-specific IgG showed lower fucosylation compared with total IgG at baseline, and most of the vaccine-induced proliferating blood CD4+ T cells did not express CCR5 and α4β7, markers associated with HIV target cells. After SHIV challenge, both routes of vaccination conferred significant and equivalent protection, with 40% of animals remaining uninfected at the end of six weekly repeated challenges with an estimated efficacy of 68% per exposure. Induction of envelope-specific IgG correlated positively with G1FB glycosylation, and G2S2F glycosylation correlated negatively with protection. Vaccine-induced TNF-α+ IFN-γ+ CD8+ T cells and TNF-α+ CD4+ T cells expressing low levels of CCR5 in the rectum at prechallenge were associated with decreased risk of SHIV acquisition. These results demonstrate that the clade C MVA/CycP-gp120 vaccine provides heterologous protection against a tier2 SHIV rectal challenge by inducing a polyfunctional antibody response with distinct Fc glycosylation profile, as well as cytotoxic CD8 T cell response and CCR5-negative T helper response in the rectum.
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Affiliation(s)
- Anusmita Sahoo
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Andrew T Jones
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Narayanaiah Cheedarla
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Sailaja Gangadhara
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Vicky Roy
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Tiffany M Styles
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Ayalnesh Shiferaw
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Korey L Walter
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - LaTonya D Williams
- Department of Surgery, Duke University Medical School, Duke University, Durham, NC 27710, USA
| | - Xiaoying Shen
- Department of Surgery, Duke University Medical School, Duke University, Durham, NC 27710, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, San Diego, CA 92121, USA
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, San Diego, CA 92121, USA
| | - Samantha Burton
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Lasanajak Yi
- Department of Biochemistry, Emory Glycomics and Molecular Interactions Core (EGMIC), School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Xuezheng Song
- Department of Biochemistry, Emory Glycomics and Molecular Interactions Core (EGMIC), School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Zhaohui S Qin
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Cynthia A Derdeyn
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, San Diego, CA 92121, USA
| | - John D Clements
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 8638, USA
| | - Raghavan Varadarajan
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, Karnataka 560012, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, Karnataka 560012, India
| | - Georgia D Tomaras
- Department of Surgery, Duke University Medical School, Duke University, Durham, NC 27710, USA
| | - Pamela A Kozlowski
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Rama Rao Amara
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
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20
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Tay W, Barnidge D, Sakrikar D, Harding S, Sherman M, Cheedarla N, Neish A. T042 Automated EXENT® mass spectrometry for the qualitative assessment of monoclonal immunoglobulins in urine. Clin Chim Acta 2022. [DOI: 10.1016/j.cca.2022.04.279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Sahoo A, Hodge EA, LaBranche CC, Styles TM, Shen X, Cheedarla N, Shiferaw A, Ozorowski G, Lee WH, Ward AB, Tomaras GD, Montefiori DC, Irvine DJ, Lee KK, Amara RR. Structure-guided changes at the V2 apex of HIV-1 clade C trimer enhance elicitation of autologous neutralizing and broad V1V2-scaffold antibodies. Cell Rep 2022; 38:110436. [PMID: 35235790 PMCID: PMC8982139 DOI: 10.1016/j.celrep.2022.110436] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/13/2021] [Accepted: 02/03/2022] [Indexed: 01/01/2023] Open
Abstract
HIV-1 clade C envelope immunogens that elicit both neutralizing and non-neutralizing V1V2-scaffold-specific antibodies (protective correlates from RV144 human trial) are urgently needed due to the prevalence of this clade in the most impacted regions worldwide. To achieve this, we introduce structure-guided changes followed by consensus-C-sequence-guided optimizations at the V2 region to generate UFO-v2-RQH173 trimer. This improves the abundance of well-formed trimers. Following the immunization of rabbits, the wild-type protein fails to elicit any autologous neutralizing antibodies, but UFO-v2-RQH173 elicits both autologous neutralizing and broad V1V2-scaffold antibodies. The variant with a 173Y modification in the V2 region, most prevalent among HIV-1 sequences, shows decreased ability in displaying a native-like V1V2 epitope with time in vitro and elicited antibodies with lower neutralizing and higher V1V2-scaffold activities. Our results identify a stabilized clade C trimer capable of eliciting improved neutralizing and V1V2-scaffold antibodies and reveal the importance of the V2 region in tuning this.
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Affiliation(s)
- Anusmita Sahoo
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Edgar A Hodge
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Celia C LaBranche
- Department of Surgery, Duke University Medical School, Duke University, Durham, NC 27710, USA
| | - Tiffany M Styles
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Xiaoying Shen
- Department of Surgery, Duke University Medical School, Duke University, Durham, NC 27710, USA
| | - Narayanaiah Cheedarla
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Ayalnesh Shiferaw
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, San Diego, CA 92121, USA
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, San Diego, CA 92121, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, San Diego, CA 92121, USA
| | - Georgia D Tomaras
- Department of Surgery, Duke University Medical School, Duke University, Durham, NC 27710, USA
| | - David C Montefiori
- Department of Surgery, Duke University Medical School, Duke University, Durham, NC 27710, USA
| | - Darrell J Irvine
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Rama Rao Amara
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA.
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22
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Cheedarla N, Verkerke HP, Potlapalli S, McLendon KB, Patel A, Frank F, Damhorst GL, Wu H, O’Sick WH, Graciaa D, Hudaib F, Alter DN, Bryksin J, Ortlund EA, Guarner J, Auld S, Shah S, Lam W, Mattoon D, Johnson JM, Wilson DH, Dhodapkar MV, Stowell SR, Neish AS, Roback JD. Rapid, high throughput, automated detection of SARS-CoV-2 neutralizing antibodies against native-like vaccine and delta variant spike trimers. Res Sq 2022:rs.3.rs-1322411. [PMID: 35194599 PMCID: PMC8863158 DOI: 10.21203/rs.3.rs-1322411/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Traditional cellular and live-virus methods for detection of SARS-CoV-2 neutralizing antibodies (nAbs) are labor- and time-intensive, and thus not suited for routine use in the clinical lab to predict vaccine efficacy and natural immune protection. Here, we report the development and validation of a rapid, high throughput method for measuring SARS-CoV-2 nAbs against native-like trimeric spike proteins. This assay uses a blockade of hACE-2 binding (BoAb) approach in an automated digital immunoassay on the Quanterix HD-X platform. BoAb assays using vaccine and delta variant viral strains showed strong correlation with cell-based pseudovirus and live-virus neutralization activity. Importantly, we were able to detect similar patterns of delta variant resistance to neutralization in samples with paired vaccine and delta variant BoAb measurements. Finally, we screened clinical samples from patients with or without evidence of SARS-CoV-2 exposure by a single-dilution screening version of our assays, finding significant nAb activity only in exposed individuals. In principle, these assays offer a rapid, robust, and scalable alternative to time-, skill-, and cost-intensive standard methods for measuring SARS-CoV-2 nAb levels.
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Affiliation(s)
- Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
- These authors contributed equally as a first authors
| | - Hans P. Verkerke
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
- These authors contributed equally as a first authors
| | - Sindhu Potlapalli
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kaleb Benjamin McLendon
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anamika Patel
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Filipp Frank
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Gregory L. Damhorst
- Department of Medicine, Division of infectious diseases, Emory University, Atlanta, GA 30322, USA
| | - Huixia Wu
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - William Henry O’Sick
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Daniel Graciaa
- Department of Medicine, Division of infectious diseases, Emory University, Atlanta, GA 30322, USA
| | - Fuad Hudaib
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - David N Alter
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jeannette Bryksin
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Eric A. Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jeanette Guarner
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sara Auld
- Department of Medicine, Division of infectious diseases, Emory University, Atlanta, GA 30322, USA
| | - Sarita Shah
- Department of Medicine, Division of infectious diseases, Emory University, Atlanta, GA 30322, USA
- Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Wilbur Lam
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Dawn Mattoon
- Quanterix Corporation, 900 Middlesex Turnpike, Billerica, MA 01821
| | - Joseph M Johnson
- Quanterix Corporation, 900 Middlesex Turnpike, Billerica, MA 01821
| | - David H Wilson
- Quanterix Corporation, 900 Middlesex Turnpike, Billerica, MA 01821
| | | | - Sean R. Stowell
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Andrew S. Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John D. Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
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23
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Cheedarla N, Verkerke HP, Potlapalli S, McLendon KB, Patel A, Frank F, Damhorst GL, Wu H, Oâ Sick WH, Graciaa D, Hudaib F, Alter DN, Bryksin J, Ortlund EA, Guarner J, Auld S, Shah S, Lam W, Mattoon D, Johnson JM, Wilson DH, Dhodapkar MV, Stowell SR, Neish AS, Roback JD. Rapid, high throughput, automated detection of SARS-CoV-2 neutralizing antibodies against native-like vaccine and delta variant spike trimers. medRxiv 2022:2022.02.01.22270279. [PMID: 35132426 PMCID: PMC8820678 DOI: 10.1101/2022.02.01.22270279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Traditional cellular and live-virus methods for detection of SARS-CoV-2 neutralizing antibodies (nAbs) are labor- and time-intensive, and thus not suited for routine use in the clinical lab to predict vaccine efficacy and natural immune protection. Here, we report the development and validation of a rapid, high throughput method for measuring SARS-CoV-2 nAbs against native-like trimeric spike proteins. This assay uses a blockade of hACE-2 binding (BoAb) approach in an automated digital immunoassay on the Quanterix HD-X platform. BoAb assays using vaccine and delta variant viral strains showed strong correlation with cell-based pseudovirus and live-virus neutralization activity. Importantly, we were able to detect similar patterns of delta variant resistance to neutralization in samples with paired vaccine and delta variant BoAb measurements. Finally, we screened clinical samples from patients with or without evidence of SARS-CoV-2 exposure by a single-dilution screening version of our assays, finding significant nAb activity only in exposed individuals. In principle, these assays offer a rapid, robust, and scalable alternative to time-, skill-, and cost-intensive standard methods for measuring SARS-CoV-2 nAb levels.
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24
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Routhu NK, Cheedarla N, Bollimpelli VS, Gangadhara S, Edara VV, Lai L, Sahoo A, Shiferaw A, Styles TM, Floyd K, Fischinger S, Atyeo C, Shin SA, Gumber S, Kirejczyk S, Dinnon KH, Shi PY, Menachery VD, Tomai M, Fox CB, Alter G, Vanderford TH, Gralinski L, Suthar MS, Amara RR. SARS-CoV-2 RBD trimer protein adjuvanted with Alum-3M-052 protects from SARS-CoV-2 infection and immune pathology in the lung. Nat Commun 2021; 12:3587. [PMID: 34117252 PMCID: PMC8196016 DOI: 10.1038/s41467-021-23942-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/26/2021] [Indexed: 02/06/2023] Open
Abstract
There is a great need for the development of vaccines that induce potent and long-lasting protective immunity against SARS-CoV-2. Multimeric display of the antigen combined with potent adjuvant can enhance the potency and longevity of the antibody response. The receptor binding domain (RBD) of the spike protein is a primary target of neutralizing antibodies. Here, we developed a trimeric form of the RBD and show that it induces a potent neutralizing antibody response against live virus with diverse effector functions and provides protection against SARS-CoV-2 challenge in mice and rhesus macaques. The trimeric form induces higher neutralizing antibody titer compared to monomer with as low as 1μg antigen dose. In mice, adjuvanting the protein with a TLR7/8 agonist formulation alum-3M-052 induces 100-fold higher neutralizing antibody titer and superior protection from infection compared to alum. SARS-CoV-2 infection causes significant loss of innate cells and pathology in the lung, and vaccination protects from changes in innate cells and lung pathology. These results demonstrate RBD trimer protein as a suitable candidate for vaccine against SARS-CoV-2.
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Affiliation(s)
- Nanda Kishore Routhu
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
| | - Narayanaiah Cheedarla
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
| | - Venkata Satish Bollimpelli
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
| | - Sailaja Gangadhara
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
| | - Venkata Viswanadh Edara
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA
| | - Lilin Lai
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA
| | - Anusmita Sahoo
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
| | - Ayalnesh Shiferaw
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
| | - Tiffany M Styles
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
| | - Katharine Floyd
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Caroline Atyeo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Sally A Shin
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Sanjeev Gumber
- Division of Pathology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Shannon Kirejczyk
- Division of Pathology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Kenneth H Dinnon
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Vineet D Menachery
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Mark Tomai
- 3M Corporate Research Materials Laboratory, Saint Paul, MN, USA
| | | | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Thomas H Vanderford
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Lisa Gralinski
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Mehul S Suthar
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA
| | - Rama Rao Amara
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.
- Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA.
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25
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Routhu NK, Cheedarla N, Gangadhara S, Bollimpelli VS, Boddapati AK, Shiferaw A, Rahman SA, Sahoo A, Edara VV, Lai L, Floyd K, Wang S, Fischinger S, Atyeo C, Shin SA, Gumber S, Kirejczyk S, Cohen J, Jean SM, Wood JS, Connor-Stroud F, Stammen RL, Upadhyay AA, Pellegrini K, Montefiori D, Shi PY, Menachery VD, Alter G, Vanderford TH, Bosinger SE, Suthar MS, Amara RR. A modified vaccinia Ankara vector-based vaccine protects macaques from SARS-CoV-2 infection, immune pathology, and dysfunction in the lungs. Immunity 2021; 54:542-556.e9. [PMID: 33631118 PMCID: PMC7859620 DOI: 10.1016/j.immuni.2021.02.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/04/2020] [Accepted: 01/29/2021] [Indexed: 02/07/2023]
Abstract
A combination of vaccination approaches will likely be necessary to fully control the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Here, we show that modified vaccinia Ankara (MVA) vectors expressing membrane-anchored pre-fusion stabilized spike (MVA/S) but not secreted S1 induced strong neutralizing antibody responses against SARS-CoV-2 in mice. In macaques, the MVA/S vaccination induced strong neutralizing antibodies and CD8+ T cell responses, and conferred protection from SARS-CoV-2 infection and virus replication in the lungs as early as day 2 following intranasal and intratracheal challenge. Single-cell RNA sequencing analysis of lung cells on day 4 after infection revealed that MVA/S vaccination also protected macaques from infection-induced inflammation and B cell abnormalities and lowered induction of interferon-stimulated genes. These results demonstrate that MVA/S vaccination induces neutralizing antibodies and CD8+ T cells in the blood and lungs and is a potential vaccine candidate for SARS-CoV-2.
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Affiliation(s)
- Nanda Kishore Routhu
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Narayanaiah Cheedarla
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Sailaja Gangadhara
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Venkata Satish Bollimpelli
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Arun K. Boddapati
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Pathology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Ayalnesh Shiferaw
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Sheikh Abdul Rahman
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Anusmita Sahoo
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Venkata Viswanadh Edara
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Lilin Lai
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Katharine Floyd
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Shelly Wang
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | | | - Caroline Atyeo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Sally A. Shin
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Sanjeev Gumber
- Division of Pathology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Shannon Kirejczyk
- Division of Pathology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Joyce Cohen
- Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Sherrie M. Jean
- Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Jennifer S. Wood
- Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Fawn Connor-Stroud
- Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Rachelle L. Stammen
- Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Amit A. Upadhyay
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Kathryn Pellegrini
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - David Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Vineet D. Menachery
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Thomas H. Vanderford
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Steven E. Bosinger
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Pathology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Mehul S. Suthar
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Rama Rao Amara
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA,Corresponding author
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26
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Babu H, Ambikan AT, Gabriel EE, Svensson Akusjärvi S, Palaniappan AN, Sundaraj V, Mupanni NR, Sperk M, Cheedarla N, Sridhar R, Tripathy SP, Nowak P, Hanna LE, Neogi U. Systemic Inflammation and the Increased Risk of Inflamm-Aging and Age-Associated Diseases in People Living With HIV on Long Term Suppressive Antiretroviral Therapy. Front Immunol 2019; 10:1965. [PMID: 31507593 PMCID: PMC6718454 DOI: 10.3389/fimmu.2019.01965] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/05/2019] [Indexed: 12/19/2022] Open
Abstract
The ART program in low- and middle-income countries (LMIC) like India, follows a public health approach with a standardized regimen for all people living with HIV (PLHIV). Based on the evidence from high-income countries (HIC), the risk of an enhanced, and accentuated onset of premature-aging or age-related diseases has been observed in PLHIV. However, very limited data is available on residual inflammation and immune activation in the populations who are on first-generation anti-HIV drugs like zidovudine and lamivudine that have more toxic side effects. Therefore, the aim of the present study was to evaluate the levels of systemic inflammation and understand the risk of age-associated diseases in PLHIV on long-term suppressive ART using a large number of biomarkers of inflammation and immune activation. Blood samples were obtained from therapy naïve PLHIV (Pre-ART, n = 43), PLHIV on ART for >5 years (ART, n = 53), and HIV-negative healthy controls (HIVNC, n = 41). Samples were analyzed for 92 markers of inflammation, sCD14, sCD163, and telomere length. Several statistical tests were performed to compare the groups under study. Multivariate linear regression was used to investigate the associations. Despite a median duration of 8 years of successful ART, sCD14 (p < 0.001) and sCD163 (p = 0.04) levels continued to be significantly elevated in ART group as compared to HIVNC. Eleven inflammatory markers, including 4E-BP1, ADA, CCL23, CD5, CD8A, CST5, MMP1, NT3, SLAMF1, TRAIL, and TRANCE, were found to be significantly different (p < 0.05) between the groups. Many of these markers are associated with age-related co-morbidities including cardiovascular disease, neurocognitive decline and some of these markers are being reported for the first time in the context of HIV-induced inflammation. Linear regression analysis showed a significant negative association between HIV-1-positivity and telomere length (p < 0.0001). In ART-group CXCL1 (p = 0.048) and TGF-α (p = 0.026) showed a significant association with the increased telomere length and IL-10RA was significantly associated with decreased telomere length (p = 0.042). This observation warrants further mechanistic studies to generate evidence to highlight the need for enhanced treatment monitoring and special interventions in HIV-infected individuals.
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Affiliation(s)
- Hemalatha Babu
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (ICMR), Chennai, India
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anoop T. Ambikan
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Erin E. Gabriel
- Department of Medical Epidemiology and Biostatistics, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sara Svensson Akusjärvi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Naveen Reddy Mupanni
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maike Sperk
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Narayanaiah Cheedarla
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (ICMR), Chennai, India
| | | | - Srikanth P. Tripathy
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (ICMR), Chennai, India
| | - Piotr Nowak
- Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Luke Elizabeth Hanna
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (ICMR), Chennai, India
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
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27
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Nesakumar M, Haribabu H, Cheedarla N, Karunaianantham R, Kailasam N, Sathyamurthi P, Selvachithiram M, Tripathy SP, Hanna LE. Transmitted HIV-1 Drug Resistance in a Treatment-Naive Cohort of Recently Infected Individuals from Chennai, India. AIDS Res Hum Retroviruses 2019; 35:775-779. [PMID: 31001987 DOI: 10.1089/aid.2019.0022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A cross-sectional study was undertaken to examine the prevalence and pattern of HIV drug resistance mutations (DRMs) among recently HIV-1-infected and antiretroviral therapy (ART)-naive individuals from Chennai, South India. The HIV-1 pol gene encompassing the protease and reverse transcriptase (RT) regions were analyzed from 53 ART-naive HIV-1-infected individuals using an in-house method for identifying DRMs by genotyping. The overall prevalence of transmitted drug resistance (TDR) was found to be 11.3% (6/53), which is categorized as moderate level (5.0%-15.0%) of TDR according to the World Health Organization (WHO) survey guidelines. Surveillance drug resistance mutations to non-nucleoside reverse transcriptase inhibitors (NNRTI) were observed in 8.3% (n = 4) of the 48 RT sequences analyzed. No major DRMs related to the protease and nucleoside reverse transcriptase inhibitor (NRTIs) class of drugs were identified.
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Affiliation(s)
- Manohar Nesakumar
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Hemalatha Haribabu
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Narayanaiah Cheedarla
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Ramesh Karunaianantham
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | | | - Pattabiraman Sathyamurthi
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Murugesan Selvachithiram
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Srikanth Prasad Tripathy
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Luke Elizabeth Hanna
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
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28
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Cheedarla N, Sundaramurthi JC, Hemalatha B, Anangi B, Nesakumar M, Ashokkumar M, Vidya Vijayan K, Tripathy SP, Swaminathan S, Vaniambadi SK, Ramanathan DV, Hanna LE. Mapping of Neutralizing Antibody Epitopes on the Envelope of Viruses Obtained from Plasma Samples Exhibiting Broad Cross-Clade Neutralization Potential Against HIV-1. AIDS Res Hum Retroviruses 2019; 35:169-184. [PMID: 30328700 DOI: 10.1089/aid.2018.0224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Several broadly neutralizing antibodies (bNAbs) that can target HIV strains with large degrees of variability have recently been identified. However, efforts to induce synthesis of such bNAbs that can protect against HIV infection have not met with much success. Identification of specific epitopes encoded in the HIV-1 envelope (Env) that can direct the host to synthesize bNAbs remains a challenge. In a previous study, we identified 12 antiretroviral therapy-naive HIV-1-infected individuals whose plasma exhibited broad cross-clade neutralization property against different clades of HIV-1. In this study, we sequenced the full-length HIV-1 gp160 from 11 of these individuals and analyzed the sequences to identify bNAb epitopes. We identified critical residues in the viral envelopes that contribute to the formation of conformational epitopes and possibly induce the production of bNAbs, using in silico methods. We found that many of the sequences had conserved glycans at positions N160 (10/11) and N332 (9/11), which are known to be critical for the binding of PG9/PG16-like and PGT128-like bNAbs, respectively. We also observed conservation of critical glycans at positions N234 and N276 critical for the interaction with CD4 binding site bNAbs in 8/11 and 11/11 sequences, respectively. We modeled the three-dimensional structure of the 11 HIV-1 envelopes and found that though each had structural differences, the critical residues were mostly present on the surface of the Env structures. The identified critical residues are proposed as candidates for further evaluation as bNAb epitopes.
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Affiliation(s)
- Narayanaiah Cheedarla
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, Chennai, India
| | | | - Babu Hemalatha
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, Chennai, India
| | - Brahmaiah Anangi
- Molecular Virology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Manohar Nesakumar
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, Chennai, India
| | - Manickam Ashokkumar
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, Chennai, India
| | - K.K. Vidya Vijayan
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, Chennai, India
| | | | - Soumya Swaminathan
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, Chennai, India
| | | | | | - Luke Elizabeth Hanna
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, Chennai, India
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29
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Cheedarla N, Hemalatha B, Anangi B, Muthuramalingam K, Selvachithiram M, Sathyamurthi P, Kailasam N, Varadarajan R, Swaminathan S, Tripathy SP, Vaniambadi SK, Vadakkupattu DR, Hanna LE. Evolution of Neutralization Response in HIV-1 Subtype C-Infected Individuals Exhibiting Broad Cross-Clade Neutralization of HIV-1 Strains. Front Immunol 2018; 9:618. [PMID: 29662494 PMCID: PMC5890096 DOI: 10.3389/fimmu.2018.00618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 03/12/2018] [Indexed: 01/04/2023] Open
Abstract
Strain-specific neutralizing antibodies develop in all human immunodeficiency virus type 1 (HIV-1)-infected individuals. However, only 10–30% of infected individuals produce broadly neutralizing antibodies (bNAbs). Identification and characterization of these bNAbs and understanding their evolution dynamics are critical for obtaining useful clues for the development of an effective HIV vaccine. Very recently, we published a study in which we identified 12 HIV-1 subtype C-infected individuals from India whose plasma showed potent and broad cross-clade neutralization (BCN) ability (1). In the present study, we report our findings on the evolution of host bNAb response over a period of 4 years in a subset of these individuals. Three of the five individuals (NAB033, NAB059, and NAB065) demonstrated a significant increase (p < 0.05) in potency. Interestingly, two of the three samples also showed a significant increase in CD4 binding site-specific antibody response, maintained stable CD4+ T cell counts (>350 cells/mm3) and continued to remain ART-naïve for more than 10 years after initial diagnosis, implying a strong clinical correlation with the development and evolution of broadly neutralizing antibody response against HIV-1.
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Affiliation(s)
- Narayanaiah Cheedarla
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, Chennai, India
| | - Babu Hemalatha
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, Chennai, India
| | - Brahmaiah Anangi
- Molecular Virology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | | | | | | | | | | | - Soumya Swaminathan
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, Chennai, India
| | | | | | | | - Luke Elizabeth Hanna
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, Chennai, India
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30
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Cheedarla N, Precilla KL, Babu H, Vijayan KKV, Ashokkumar M, Chandrasekaran P, Kailasam N, Sundaramurthi JC, Swaminathan S, Buddolla V, Vaniambadi SK, Ramanathan VD, Hanna LE. Broad and potent cross clade neutralizing antibodies with multiple specificities in the plasma of HIV-1 subtype C infected individuals. Sci Rep 2017; 7:46557. [PMID: 28436427 PMCID: PMC5402285 DOI: 10.1038/srep46557] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 03/21/2017] [Indexed: 11/09/2022] Open
Abstract
Broadly Cross clade Neutralizing (BCN) antibodies are recognized as potential therapeutic tools and leads for the design of a vaccine that can protect human beings against various clades of Human Immunodeficiency Virus (HIV). In the present study, we screened plasma of 88 HIV-1 infected ART naïve individuals for their neutralization potential using a standard panel of 18 pseudoviruses belonging to different subtypes and different levels of neutralization. We identified 12 samples with good breadth of neutralization (neutralized >90% of the viruses). Four of these samples neutralized even the difficult-to-neutralize tier-3 pseudoviruses with great potency (GMT > 600). Analysis of neutralization specificities indicated that four samples had antibodies with multiple epitope binding specificities, viz. CD4-binding site (CD4BS), glycans in the V1/V2 and V3 regions and membrane proximal external region (MPER). Our findings indicate the strong possibility of identifying highly potent bNAbs with known or novel specificities from HIV-1 subtype C infected individuals from India that can be exploited as therapeutic tools or lead molecules for the identification of potential epitopes for design of a protective HIV-1 vaccine.
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Affiliation(s)
- Narayanaiah Cheedarla
- HIV/AIDS Division, Department of Clinical Research, National Institute for Research in Tuberculosis, Clinical Research, Chennai, 600031, India
| | - K Lucia Precilla
- HIV/AIDS Division, Department of Clinical Research, National Institute for Research in Tuberculosis, Clinical Research, Chennai, 600031, India
| | - Hemalatha Babu
- HIV/AIDS Division, Department of Clinical Research, National Institute for Research in Tuberculosis, Clinical Research, Chennai, 600031, India
| | - K K Vidya Vijayan
- HIV/AIDS Division, Department of Clinical Research, National Institute for Research in Tuberculosis, Clinical Research, Chennai, 600031, India
| | - Manickam Ashokkumar
- HIV/AIDS Division, Department of Clinical Research, National Institute for Research in Tuberculosis, Clinical Research, Chennai, 600031, India
| | - Padmapriyadarsini Chandrasekaran
- HIV/AIDS Division, Department of Clinical Research, National Institute for Research in Tuberculosis, Clinical Research, Chennai, 600031, India
| | | | - Jagadish Chandrabose Sundaramurthi
- HIV/AIDS Division, Department of Clinical Research, National Institute for Research in Tuberculosis, Clinical Research, Chennai, 600031, India
| | - Soumya Swaminathan
- HIV/AIDS Division, Department of Clinical Research, National Institute for Research in Tuberculosis, Clinical Research, Chennai, 600031, India
| | - Viswanath Buddolla
- Department of Bionanotechnology, Gachon University, San 65, Bokjeong-Dong, Sujeong-Gu, Seongnam-Si, Gyeonggi- Do, 461701, Republic of Korea
| | | | - V D Ramanathan
- HIV/AIDS Division, Department of Clinical Research, National Institute for Research in Tuberculosis, Clinical Research, Chennai, 600031, India
| | - Luke Elizabeth Hanna
- HIV/AIDS Division, Department of Clinical Research, National Institute for Research in Tuberculosis, Clinical Research, Chennai, 600031, India
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Bachu M, Mukthey AB, Murali RV, Cheedarla N, Mahadevan A, Shankar SK, Satish KS, Kundu TK, Ranga U. Sequence insertions in the HIV type 1 subtype C viral promoter predominantly generate an additional NF-κB binding site. AIDS Res Hum Retroviruses 2012; 28:1362-8. [PMID: 22332607 DOI: 10.1089/aid.2011.0388] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
After screening a large number of clinical samples of HIV-1 subtype C in India, a subset of viral strains containing sequence insertions upstream of the viral enhancer has been identified. The sequence insertions contained binding sites for at least two different transcription factors NF-κB and RBEIII, importantly, in a mutually exclusive fashion. Furthermore, while some of the viral strains contained insertions of κB-like sites, a few others contained dual insertions of the RBEIII and κB sites together but only one of the two was intact. NF-κB acquisition appears to be the most common phenotype unique for subtype C with nearly half of the variant strains containing such insertions. Given that subtype C already contains three functional NF-κB sites in the viral enhancer, acquisition of a fourth NF-κB motif in some variant viral strains is intriguing. Further investigation is warranted to examine the significance of the sequence insertions for the replicative fitness of the variant viral strains.
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Affiliation(s)
- Mahesh Bachu
- HIV-AIDS Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
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