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Bradley CC, Wang C, Gordon AJE, Wen AX, Luna PN, Cooke MB, Kohrn BF, Kennedy SR, Avadhanula V, Piedra PA, Lichtarge O, Shaw CA, Ronca SE, Herman C. Targeted accurate RNA consensus sequencing (tARC-seq) reveals mechanisms of replication error affecting SARS-CoV-2 divergence. Nat Microbiol 2024:10.1038/s41564-024-01655-4. [PMID: 38649410 DOI: 10.1038/s41564-024-01655-4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/28/2024] [Indexed: 04/25/2024]
Abstract
RNA viruses, like SARS-CoV-2, depend on their RNA-dependent RNA polymerases (RdRp) for replication, which is error prone. Monitoring replication errors is crucial for understanding the virus's evolution. Current methods lack the precision to detect rare de novo RNA mutations, particularly in low-input samples such as those from patients. Here we introduce a targeted accurate RNA consensus sequencing method (tARC-seq) to accurately determine the mutation frequency and types in SARS-CoV-2, both in cell culture and clinical samples. Our findings show an average of 2.68 × 10-5 de novo errors per cycle with a C > T bias that cannot be solely attributed to APOBEC editing. We identified hotspots and cold spots throughout the genome, correlating with high or low GC content, and pinpointed transcription regulatory sites as regions more susceptible to errors. tARC-seq captured template switching events including insertions, deletions and complex mutations. These insights shed light on the genetic diversity generation and evolutionary dynamics of SARS-CoV-2.
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Affiliation(s)
- Catherine C Bradley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor College of Medicine Medical Scientist Training Program, Houston, TX, USA
- Robert and Janice McNair Foundation/ McNair Medical Institute M.D./Ph.D. Scholars program, Houston, TX, USA
| | - Chen Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Alasdair J E Gordon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Alice X Wen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor College of Medicine Medical Scientist Training Program, Houston, TX, USA
- Robert and Janice McNair Foundation/ McNair Medical Institute M.D./Ph.D. Scholars program, Houston, TX, USA
| | - Pamela N Luna
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Matthew B Cooke
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Brendan F Kohrn
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Scott R Kennedy
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shannon E Ronca
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Feigin Biosafety Level 3 Facility, Texas Children's Hospital, Houston, TX, USA
- National School of Tropical Medicine, Department of Pediatrics Tropical Medicine, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.
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Moline HL, Tannis A, Toepfer AP, Williams JV, Boom JA, Englund JA, Halasa NB, Staat MA, Weinberg GA, Selvarangan R, Michaels MG, Sahni LC, Klein EJ, Stewart LS, Schlaudecker EP, Szilagyi PG, Schuster JE, Goldstein L, Musa S, Piedra PA, Zerr DM, Betters KA, Rohlfs C, Albertin C, Banerjee D, McKeever ER, Kalman C, Clopper BR, McMorrow ML, Dawood FS. Early Estimate of Nirsevimab Effectiveness for Prevention of Respiratory Syncytial Virus-Associated Hospitalization Among Infants Entering Their First Respiratory Syncytial Virus Season - New Vaccine Surveillance Network, October 2023-February 2024. MMWR Morb Mortal Wkly Rep 2024; 73:209-214. [PMID: 38457312 PMCID: PMC10932582 DOI: 10.15585/mmwr.mm7309a4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2024]
Abstract
Respiratory syncytial virus (RSV) is the leading cause of hospitalization among infants in the United States. In August 2023, CDC's Advisory Committee on Immunization Practices recommended nirsevimab, a long-acting monoclonal antibody, for infants aged <8 months to protect against RSV-associated lower respiratory tract infection during their first RSV season and for children aged 8-19 months at increased risk for severe RSV disease. In phase 3 clinical trials, nirsevimab efficacy against RSV-associated lower respiratory tract infection with hospitalization was 81% (95% CI = 62%-90%) through 150 days after receipt; post-introduction effectiveness has not been assessed in the United States. In this analysis, the New Vaccine Surveillance Network evaluated nirsevimab effectiveness against RSV-associated hospitalization among infants in their first RSV season during October 1, 2023-February 29, 2024. Among 699 infants hospitalized with acute respiratory illness, 59 (8%) received nirsevimab ≥7 days before symptom onset. Nirsevimab effectiveness was 90% (95% CI = 75%-96%) against RSV-associated hospitalization with a median time from receipt to symptom onset of 45 days (IQR = 19-76 days). The number of infants who received nirsevimab was too low to stratify by duration from receipt; however, nirsevimab effectiveness is expected to decrease with increasing time after receipt because of antibody decay. Although nirsevimab uptake and the interval from receipt of nirsevimab were limited in this analysis, this early estimate supports the current nirsevimab recommendation for the prevention of severe RSV disease in infants. Infants should be protected by maternal RSV vaccination or infant receipt of nirsevimab.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - New Vaccine Surveillance Network Product Effectiveness Collaborators
- Coronavirus and Other Respiratory Viruses Division, National Center for Immunization and Respiratory Diseases, CDC; UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Texas Children’s Hospital, Houston, Texas; Baylor College of Medicine, Houston, Texas; Department of Pediatrics, Seattle Children’s Hospital, Seattle, Washington; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee; Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio; Department of Pediatrics, University of Rochester Medical Center and University of Rochester–Golisano Children’s Hospital, Rochester, New York; Department of Pathology and Laboratory Medicine, Children’s Mercy Hospital, Kansas City, Missouri; Department of Pediatrics Children’s Mercy Hospital, Kansas City, Missouri
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3
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Toepfer AP, Amarin JZ, Spieker AJ, Stewart LS, Staat MA, Schlaudecker EP, Weinberg GA, Szilagyi PG, Englund JA, Klein EJ, Michaels MG, Williams JV, Selvarangan R, Harrison CJ, Lively JY, Piedra PA, Avadhanula V, Rha B, Chappell J, McMorrow M, Moline H, Halasa NB. Seasonality, clinical characteristics, and outcomes of respiratory syncytial virus disease by subtype among children less than five years old, New Vaccine Surveillance Network, United States, 2016-2020. Clin Infect Dis 2024:ciae085. [PMID: 38366649 DOI: 10.1093/cid/ciae085] [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: 12/14/2023] [Revised: 02/06/2024] [Accepted: 02/13/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is a leading cause of acute respiratory illnesses (ARI) in children. RSV can be broadly categorized into two major subtypes (A and B). RSV subtypes have been known to co-circulate with variability in different regions of the world. Clinical associations with viral subtype have been studied among children with conflicting findings such that no conclusive relationships between RSV subtype and severity have been established. METHODS During 2016-2020, children <5 years old were enrolled in prospective surveillance in the emergency department (ED) or inpatient (IP) settings from seven U.S. pediatric medical centers. Surveillance data collection included parent/guardian interviews, chart reviews, and collection of mid-turbinate nasal +/- throat swabs for RSV (RSV-A, RSV-B, and Untyped) by reverse transcription polymerase chain reaction (RT-PCR). RESULTS Among 6398 RSV-positive children <5 years old, 3424 (54%) had subtype RSV-A infections, 2602 (41%) had subtype RSV-B infections, and 272 (5%) were not typed, inconclusive, or mixed infections. In both adjusted and unadjusted analyses, RSV-A-positive children were more likely to be hospitalized, as well as when restricted to <1 year. By season, RSV-A and RSV-B co-circulated in varying levels, with one subtype dominating proportionally. CONCLUSION Findings indicate that RSV-A and RSV-B may only be marginally clinically distinguishable but both subtypes are associated with medically attended illness in children <5 years old. Furthermore, circulation of RSV subtypes varies substantially each year, seasonally and geographically. With introduction of new RSV prevention products, this highlights the importance of continued monitoring of RSV-A and RSV-B subtypes.
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Affiliation(s)
- Ariana P Toepfer
- Coronavirus and Other Respiratory Viruses Division, National Center for Immunization and Respiratory Diseases, CDC, Atlanta, Georgia, USA
| | - Justin Z Amarin
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Andrew J Spieker
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Laura S Stewart
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mary Allen Staat
- Division of Infectious Diseases, Cincinnati Children's Hospital, Cincinnati, Ohio, USA
| | | | - Geoffrey A Weinberg
- Department of Pediatrics, University of Rochester School of Medicine & Dentistry, Rochester, New York, USA
| | - Peter G Szilagyi
- Department of Pediatrics, University of Rochester School of Medicine & Dentistry, Rochester, New York, USA
| | - Janet A Englund
- Department of Pediatrics, Seattle Children's Hospital, Seattle, Washington, USA
| | - Eileen J Klein
- Department of Pediatrics, Seattle Children's Hospital, Seattle, Washington, USA
| | - Marian G Michaels
- UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John V Williams
- UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Rangaraj Selvarangan
- Department of Pathology and Laboratory Medicine, Children's Mercy, Kansas City, Missouri, USA
| | - Christopher J Harrison
- Department of Pathology and Laboratory Medicine, Children's Mercy, Kansas City, Missouri, USA
| | - Joana Y Lively
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, CDC, Atlanta, Georgia, USA
| | | | | | - Brian Rha
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, CDC, Atlanta, Georgia, USA
| | - James Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Meredith McMorrow
- Coronavirus and Other Respiratory Viruses Division, National Center for Immunization and Respiratory Diseases, CDC, Atlanta, Georgia, USA
- U.S. Public Health Service, Rockville, Maryland, USA
| | - Heidi Moline
- Coronavirus and Other Respiratory Viruses Division, National Center for Immunization and Respiratory Diseases, CDC, Atlanta, Georgia, USA
- U.S. Public Health Service, Rockville, Maryland, USA
| | - Natasha B Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Ashraf-Uz-Zaman M, Chua TK, Li X, Yao Y, Moku BK, Mishra CB, Avadhanula V, Piedra PA, Song Y. Design, Synthesis, X-ray Crystallography, and Biological Activities of Covalent, Non-Peptidic Inhibitors of SARS-CoV-2 Main Protease. ACS Infect Dis 2024; 10:715-731. [PMID: 38192109 PMCID: PMC10922772 DOI: 10.1021/acsinfecdis.3c00565] [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] [Indexed: 01/10/2024]
Abstract
Highly contagious SARS-CoV-2 coronavirus has infected billions of people worldwide with flu-like symptoms since its emergence in 2019. It has caused deaths of several million people. The viral main protease (Mpro) is essential for SARS-CoV-2 replication and therefore a drug target. Several series of covalent inhibitors of Mpro were designed and synthesized. Structure-activity relationship studies show that (1) several chloroacetamide- and epoxide-based compounds targeting Cys145 are potent inhibitors with IC50 values as low as 0.49 μM and (2) Cys44 of Mpro is not nucleophilic for covalent inhibitor design. High-resolution X-ray studies revealed the protein-inhibitor interactions and mechanisms of inhibition. It is of interest that Cys145 preferably attacks the more hindered Cα atom of several epoxide inhibitors. Chloroacetamide inhibitor 13 and epoxide inhibitor 30 were found to inhibit cellular SARS-CoV-2 replication with an EC68 (half-log reduction of virus titer) of 3 and 5 μM. These compounds represent new pharmacological leads for anti-SARS-CoV-2 drug development.
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Affiliation(s)
- Md Ashraf-Uz-Zaman
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Teck Khiang Chua
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Xin Li
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Yuan Yao
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Bala Krishna Moku
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Chandra Bhushan Mishra
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Vasanthi Avadhanula
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Pedro A. Piedra
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Yongcheng Song
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
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5
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Nicholson EG, Avadhanula V, Sahni LC, Ferlic‐Stark L, Maurer L, Boom JA, Piedra PA. Respiratory viral detection in the plasma and cerebrospinal fluid (CSF) of young febrile infants. Influenza Other Respir Viruses 2024; 18:e13250. [PMID: 38314065 PMCID: PMC10831571 DOI: 10.1111/irv.13250] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 02/06/2024] Open
Abstract
Background Respiratory viral infections are common in febrile infants ≤90 days. However, the detection of viruses other than enterovirus in the blood and cerebrospinal fluid (CSF) of young infants is not well defined. We sought to quantify the occurrence of respiratory viruses in the blood and CSF of febrile infants ≤90 days. Methods We conducted a nested cohort study examining plasma and CSF samples from febrile infants 15-90 days via rtPCR. The samples were tested for respiratory viruses (respiratory syncytial virus, influenza, enterovirus, parechovirus, adenovirus, bocavirus). Clinical and laboratory data were also collected to determine the presence of serious bacterial infections (SBI). Results Twenty-four percent (30 of 126) of infants had plasma/CSF specimens positive for a respiratory virus. Enterovirus and parechovirus were the most commonly detected respiratory viruses. Viral positivity was highest in plasma samples at 25% (27 of 107) compared with CSF samples at 15% (nine of 62). SBIs (specifically urinary tract infections) were less common in infants with a sample positive for a respiratory virus compared to those without a virus detected (3% vs. 26%, p = 0.008). Conclusions Our findings support the use of molecular diagnostics to include the identification of parechovirus in addition to enterovirus in febrile infants ≤90 days. Additionally, these data support the utilization of blood specimens to diagnose enterovirus and parechovirus infections in febrile infants ≤90 days.
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Affiliation(s)
- Erin G. Nicholson
- Department of Molecular Virology and MicrobiologyBaylor College of MedicineHoustonTexasUSA
- Department of PediatricsBaylor College of MedicineHoustonTexasUSA
| | - Vasanthi Avadhanula
- Department of Molecular Virology and MicrobiologyBaylor College of MedicineHoustonTexasUSA
| | - Leila C. Sahni
- Department of PediatricsBaylor College of MedicineHoustonTexasUSA
- Texas Children's HospitalHoustonTexasUSA
| | - Laura Ferlic‐Stark
- Department of Molecular Virology and MicrobiologyBaylor College of MedicineHoustonTexasUSA
| | - Lauren Maurer
- Department of Molecular Virology and MicrobiologyBaylor College of MedicineHoustonTexasUSA
| | - Julie A. Boom
- Department of PediatricsBaylor College of MedicineHoustonTexasUSA
| | - Pedro A. Piedra
- Department of Molecular Virology and MicrobiologyBaylor College of MedicineHoustonTexasUSA
- Department of PediatricsBaylor College of MedicineHoustonTexasUSA
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6
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Aloisio GM, Nagaraj D, Murray AM, Schultz EM, McBride T, Aideyan L, Nicholson EG, Henke D, Ferlic-Stark L, Rajan A, Kambal A, Johnson HL, Mosa E, Stossi F, Blutt SE, Piedra PA, Avadhanula V. Pediatric human nose organoids demonstrate greater susceptibility, epithelial responses, and cytotoxicity than adults during RSV infection. bioRxiv 2024:2024.02.01.578466. [PMID: 38352333 PMCID: PMC10862794 DOI: 10.1101/2024.02.01.578466] [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: 02/24/2024]
Abstract
Respiratory syncytial virus (RSV) is a common cause of respiratory infections, causing significant morbidity and mortality, especially in young children. Why RSV infection in children is more severe as compared to healthy adults is not fully understood. In the present study, we infect both pediatric and adult human nose organoid-air liquid interface (HNO-ALIs) cell lines with two contemporary RSV isolates and demonstrate how they differ in virus replication, induction of the epithelial cytokine response, cell injury, and remodeling. Pediatric HNO-ALIs were more susceptible to early RSV replication, elicited a greater overall cytokine response, demonstrated enhanced mucous production, and manifested greater cellular damage compared to their adult counterparts. Adult HNO-ALIs displayed enhanced mucus production and robust cytokine response that was well controlled by superior regulatory cytokine response and possibly resulted in lower cellular damage than in pediatric lines. Taken together, our data suggest substantial differences in how pediatric and adult upper respiratory tract epithelium responds to RSV infection. These differences in epithelial cellular response can lead to poor mucociliary clearance and predispose infants to a worse respiratory outcome of RSV infection.
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Affiliation(s)
- Gina M Aloisio
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Divya Nagaraj
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Ashley M Murray
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Emily M Schultz
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Trevor McBride
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Letisha Aideyan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Erin G Nicholson
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - David Henke
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Laura Ferlic-Stark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Amal Kambal
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Hannah L Johnson
- Advanced Technology Cores, Baylor College of Medicine, Houston, Texas, USA
| | - Elina Mosa
- Advanced Technology Cores, Baylor College of Medicine, Houston, Texas, USA
| | - Fabio Stossi
- Advanced Technology Cores, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Sarah E Blutt
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
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7
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Avadhanula V, Agustinho DP, Menon VK, Chemaly RF, Shah DP, Qin X, Surathu A, Doddapaneni H, Muzny DM, Metcalf GA, Cregeen SJ, Gibbs RA, Petrosino JF, Sedlazeck FJ, Piedra PA. Inter and intra-host diversity of RSV in hematopoietic stem cell transplant adults with normal and delayed viral clearance. Virus Evol 2023; 10:vead086. [PMID: 38361816 PMCID: PMC10868550 DOI: 10.1093/ve/vead086] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 12/05/2023] [Accepted: 12/22/2023] [Indexed: 02/17/2024] Open
Abstract
Respiratory syncytial virus (RSV) infection in immunocompromised individuals often leads to prolonged illness, progression to severe lower respiratory tract infection, and even death. How the host immune environment of the hematopoietic stem cell transplant (HCT) adults can affect viral genetic variation during an acute infection is not understood well. In the present study, we performed whole genome sequencing of RSV/A or RSV/B from samples collected longitudinally from HCT adults with normal (<14 days) and delayed (≥14 days) RSV clearance who were enrolled in a ribavirin trial. We determined the inter-host and intra-host genetic variation of RSV and the effect of mutations on putative glycosylation sites. The inter-host variation of RSV is centered in the attachment (G) and fusion (F) glycoprotein genes followed by polymerase (L) and matrix (M) genes. Interestingly, the overall genetic variation was constant between normal and delayed clearance groups for both RSV/A and RSV/B. Intra-host variation primarily occurred in the G gene followed by non-structural protein (NS1) and L genes; however, gain or loss of stop codons and frameshift mutations appeared only in the G gene and only in the delayed viral clearance group. Potential gain or loss of O-linked glycosylation sites in the G gene occurred both in RSV/A and RSV/B isolates. For RSV F gene, loss of N-linked glycosylation site occurred in three RSV/B isolates within an antigenic epitope. Both oral and aerosolized ribavirin did not cause any mutations in the L gene. In summary, prolonged viral shedding and immune deficiency resulted in RSV variation, especially in structural mutations in the G gene, possibly associated with immune evasion. Therefore, sequencing and monitoring of RSV isolates from immunocompromised patients are crucial as they can create escape mutants that can impact the effectiveness of upcoming vaccines and treatments.
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Affiliation(s)
| | | | - Vipin Kumar Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Roy F Chemaly
- Departments of Infectious Diseases, Infection Control & Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dimpy P Shah
- Department of Population Health Sciences, Mays Cancer Center, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anil Surathu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030,USA
| | - Harshavardhan Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ginger A Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sara Javornik Cregeen
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030,USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joseph F Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030,USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030,USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030,USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
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8
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Tisza M, Javornik Cregeen S, Avadhanula V, Zhang P, Ayvaz T, Feliz K, Hoffman KL, Clark JR, Terwilliger A, Ross MC, Cormier J, Moreno H, Wang L, Payne K, Henke D, Troisi C, Wu F, Rios J, Deegan J, Hansen B, Balliew J, Gitter A, Zhang K, Li R, Bauer CX, Mena KD, Piedra PA, Petrosino JF, Boerwinkle E, Maresso AW. Wastewater sequencing reveals community and variant dynamics of the collective human virome. Nat Commun 2023; 14:6878. [PMID: 37898601 PMCID: PMC10613200 DOI: 10.1038/s41467-023-42064-1] [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: 05/22/2023] [Accepted: 09/25/2023] [Indexed: 10/30/2023] Open
Abstract
Wastewater is a discarded human by-product, but its analysis may help us understand the health of populations. Epidemiologists first analyzed wastewater to track outbreaks of poliovirus decades ago, but so-called wastewater-based epidemiology was reinvigorated to monitor SARS-CoV-2 levels while bypassing the difficulties and pit falls of individual testing. Current approaches overlook the activity of most human viruses and preclude a deeper understanding of human virome community dynamics. Here, we conduct a comprehensive sequencing-based analysis of 363 longitudinal wastewater samples from ten distinct sites in two major cities. Critical to detection is the use of a viral probe capture set targeting thousands of viral species or variants. Over 450 distinct pathogenic viruses from 28 viral families are observed, most of which have never been detected in such samples. Sequencing reads of established pathogens and emerging viruses correlate to clinical data sets of SARS-CoV-2, influenza virus, and monkeypox viruses, outlining the public health utility of this approach. Viral communities are tightly organized by space and time. Finally, the most abundant human viruses yield sequence variant information consistent with regional spread and evolution. We reveal the viral landscape of human wastewater and its potential to improve our understanding of outbreaks, transmission, and its effects on overall population health.
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Affiliation(s)
- Michael Tisza
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sara Javornik Cregeen
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ping Zhang
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Tulin Ayvaz
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Karen Feliz
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kristi L Hoffman
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Justin R Clark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- TAILOR Labs, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Austen Terwilliger
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- TAILOR Labs, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Matthew C Ross
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Juwan Cormier
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hannah Moreno
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Li Wang
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Katelyn Payne
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David Henke
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Catherine Troisi
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Fuqing Wu
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Texas Epidemiologic Public Health Institute (TEPHI), Houston, TX, USA
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth Houston School of Public Health, Houston, 77030, USA
| | - Janelle Rios
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Texas Epidemiologic Public Health Institute (TEPHI), Houston, TX, USA
| | - Jennifer Deegan
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Texas Epidemiologic Public Health Institute (TEPHI), Houston, TX, USA
| | - Blake Hansen
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Texas Epidemiologic Public Health Institute (TEPHI), Houston, TX, USA
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth Houston School of Public Health, Houston, 77030, USA
| | | | - Anna Gitter
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Texas Epidemiologic Public Health Institute (TEPHI), Houston, TX, USA
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth Houston School of Public Health, Houston, 77030, USA
| | - Kehe Zhang
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Department of Biostatistics and Data Science, UTHealth Houston School of Public Health, Houston, TX, 77030, USA
- Center for Spatial-temporal Modeling for Applications in Population Sciences, UTHealth Houston School of Public Health, Houston, TX, 77030, USA
| | - Runze Li
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Department of Biostatistics and Data Science, UTHealth Houston School of Public Health, Houston, TX, 77030, USA
- Center for Spatial-temporal Modeling for Applications in Population Sciences, UTHealth Houston School of Public Health, Houston, TX, 77030, USA
| | - Cici X Bauer
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Texas Epidemiologic Public Health Institute (TEPHI), Houston, TX, USA
- Department of Biostatistics and Data Science, UTHealth Houston School of Public Health, Houston, TX, 77030, USA
- Center for Spatial-temporal Modeling for Applications in Population Sciences, UTHealth Houston School of Public Health, Houston, TX, 77030, USA
| | - Kristina D Mena
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Texas Epidemiologic Public Health Institute (TEPHI), Houston, TX, USA
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth Houston School of Public Health, Houston, 77030, USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Joseph F Petrosino
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Eric Boerwinkle
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
- Texas Epidemiologic Public Health Institute (TEPHI), Houston, TX, USA.
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth Houston School of Public Health, Houston, 77030, USA.
| | - Anthony W Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.
- TAILOR Labs, Baylor College of Medicine, Houston, TX, 77030, USA.
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Rezende W, Neal HE, Dutch RE, Piedra PA. The RSV F p27 peptide: current knowledge, important questions. Front Microbiol 2023; 14:1219846. [PMID: 37415824 PMCID: PMC10320223 DOI: 10.3389/fmicb.2023.1219846] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/01/2023] [Indexed: 07/08/2023] Open
Abstract
Respiratory syncytial virus (RSV) remains a leading cause of hospitalizations and death for young children and adults over 65. The worldwide impact of RSV has prioritized the search for an RSV vaccine, with most targeting the critical fusion (F) protein. However, questions remain about the mechanism of RSV entry and RSV F triggering and fusion promotion. This review highlights these questions, specifically those surrounding a cleaved 27 amino acids long peptide within F, p27.
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Affiliation(s)
- Wanderson Rezende
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, United States
| | - Hadley E. Neal
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, United States
| | - Rebecca E. Dutch
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, United States
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
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10
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Rezende W, Ye X, Angelo LS, Carisey AF, Avadhanula V, Piedra PA. The Efficiency of p27 Cleavage during In Vitro Respiratory Syncytial Virus (RSV) Infection Is Cell Line and RSV Subtype Dependent. J Virol 2023; 97:e0025423. [PMID: 37133390 PMCID: PMC10231215 DOI: 10.1128/jvi.00254-23] [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: 02/16/2023] [Accepted: 04/11/2023] [Indexed: 05/04/2023] Open
Abstract
Respiratory syncytial virus (RSV) fusion protein (F) is highly conserved between subtypes A and B (RSV/A and RSV/B). To become fully active, F precursor undergoes enzymatic cleavage to yield F1 and F2 subunits and releases a 27-amino-acid peptide (p27). Virus-cell fusion occurs when RSV F undergoes a conformational change from pre-F to post-F. Previous data show that p27 is detected on RSV F, but questions remain regarding if and how p27 affects the conformation of mature RSV F. Monoclonal antibodies against p27, site Ø (pre-F specific), and site II were used to monitor RSV F conformation by enzyme-linked immunosorbent assay (ELISA) and imaging flow cytometry. Pre-F to post-F conformational change was induced by a temperature stress test. We found that p27 cleavage efficiency was lower on sucrose-purified RSV/A (spRSV/A) than on spRSV/B. In addition, cleavage of RSV F was cell line dependent: HEp-2 cells had higher retention of p27 than did A549 cells when infected with RSV. Higher levels of p27 were also found on RSV/A-infected cells than on RSV/B-infected cells. We observed that RSV/A F with higher p27 levels could better sustain the pre-F conformation during the temperature stress challenge in both spRSV- and RSV-infected cell lines. Our findings suggest that despite F sequence similarity, p27 of RSV subtypes was cleaved with different efficiencies, which were also dependent on the cell lines used for infection. Importantly, the presence of p27 was associated with greater stability of the pre-F conformation, supporting the possibility that RSV has more than one mechanism for fusion to the host cell. IMPORTANCE RSV fusion protein (F) plays an important role in entry and viral fusion to the host cell. The F undergoes proteolytic cleavages releasing a 27-amino-acid peptide (p27) to become fully functional. The role of p27 in viral entry and the function of the partially cleaved F containing p27 has been overlooked. p27 is thought to destabilize the F trimers, and thus, there is need for a fully cleaved F. In this study, we detected p27 on purified RSV virions and on the surface of virus-infected HEp-2 and A549 cells for circulating RSV strains of both subtypes. Higher levels of partially cleaved F containing p27 better sustained the pre-F conformation during the temperature stress challenge. Our findings highlight that the cleavage efficiency of p27 is different between RSV subtypes and among cell lines and that the presence of p27 contributes to the stability of the pre-F conformation.
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Affiliation(s)
- Wanderson Rezende
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas, USA
| | - Xunyan Ye
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Avance Biosciences, Houston, Texas, USA
| | - Laura S. Angelo
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Alexandre F. Carisey
- William T. Shearer Center for Human Immunology, Texas Children’s Hospital, Houston, Texas, USA
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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11
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Avadhanula V, Creighton CJ, Ferlic-Stark L, Sucgang R, Zhang Y, Nagaraj D, Nicholson EG, Rajan A, Menon VK, Doddapaneni H, Muzny DM, Metcalf G, Cregeen SJJ, Hoffman KL, Gibbs RA, Petrosino J, Piedra PA. Longitudinal host transcriptional responses to SARS-CoV-2 infection in adults with extremely high viral load. bioRxiv 2023:2023.05.24.542181. [PMID: 37292999 PMCID: PMC10245966 DOI: 10.1101/2023.05.24.542181] [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: 06/10/2023]
Abstract
Current understanding of viral dynamics of SARS-CoV-2 and host responses driving the pathogenic mechanisms in COVID-19 is rapidly evolving. Here, we conducted a longitudinal study to investigate gene expression patterns during acute SARS-CoV-2 illness. Cases included SARS-CoV-2 infected individuals with extremely high viral loads early in their illness, individuals having low SARS-CoV-2 viral loads early in their infection, and individuals testing negative for SARS-CoV-2. We could identify widespread transcriptional host responses to SARS-CoV-2 infection that were initially most strongly manifested in patients with extremely high initial viral loads, then attenuating within the patient over time as viral loads decreased. Genes correlated with SARS-CoV-2 viral load over time were similarly differentially expressed across independent datasets of SARS-CoV-2 infected lung and upper airway cells, from both in vitro systems and patient samples. We also generated expression data on the human nose organoid model during SARS-CoV-2 infection. The human nose organoid-generated host transcriptional response captured many aspects of responses observed in the above patient samples, while suggesting the existence of distinct host responses to SARS-CoV-2 depending on the cellular context, involving both epithelial and cellular immune responses. Our findings provide a catalog of SARS-CoV-2 host response genes changing over time.
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Affiliation(s)
- Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chad J. Creighton
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Laura Ferlic-Stark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard Sucgang
- Center for Health Data Science and Analytics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Divya Nagaraj
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Erin G. Nicholson
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Vipin Kumar Menon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harshavardhan Doddapaneni
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna Marie Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ginger Metcalf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Kristi Louise Hoffman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joseph Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
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12
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Sahni LC, Naioti EA, Olson SM, Campbell AP, Michaels MG, Williams JV, Staat MA, Schlaudecker EP, McNeal MM, Halasa NB, Stewart LS, Chappell JD, Englund JA, Klein EJ, Szilagyi PG, Weinberg GA, Harrison CJ, Selvarangan R, Schuster JE, Azimi PH, Singer MN, Avadhanula V, Piedra PA, Munoz FM, Patel MM, Boom JA. Sustained Within-season Vaccine Effectiveness Against Influenza-associated Hospitalization in Children: Evidence From the New Vaccine Surveillance Network, 2015-2016 Through 2019-2020. Clin Infect Dis 2023; 76:e1031-e1039. [PMID: 35867698 DOI: 10.1093/cid/ciac577] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 01/03/2022] [Revised: 06/29/2022] [Accepted: 07/12/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Adult studies have demonstrated within-season declines in influenza vaccine effectiveness (VE); data in children are limited. METHODS We conducted a prospective, test-negative study of children 6 months through 17 years hospitalized with acute respiratory illness at 7 pediatric medical centers during the 2015-2016 through 2019-2020 influenza seasons. Case-patients were children with an influenza-positive molecular test matched by illness onset to influenza-negative control-patients. We estimated VE [100% × (1 - odds ratio)] by comparing the odds of receipt of ≥1 dose of influenza vaccine ≥14 days before illness onset among influenza-positive children to influenza-negative children. Changes in VE over time between vaccination date and illness onset date were estimated using multivariable logistic regression. RESULTS Of 8430 children, 4653 (55%) received ≥1 dose of influenza vaccine. On average, 48% were vaccinated through October and 85% through December each season. Influenza vaccine receipt was lower in case-patients than control-patients (39% vs 57%, P < .001); overall VE against hospitalization was 53% (95% confidence interval [CI]: 46, 60%). Pooling data across 5 seasons, the odds of influenza-associated hospitalization increased 4.2% (-3.2%, 12.2%) per month since vaccination, with an average VE decrease of 1.9% per month (n = 4000, P = .275). Odds of hospitalization increased 2.9% (95% CI: -5.4%, 11.8%) and 9.6% (95% CI: -7.0%, 29.1%) per month in children ≤8 years (n = 3084) and 9-17 years (n = 916), respectively. These findings were not statistically significant. CONCLUSIONS We observed minimal, not statistically significant within-season declines in VE. Vaccination following current Advisory Committee on Immunization Practices (ACIP) guidelines for timing of vaccine receipt remains the best strategy for preventing influenza-associated hospitalizations in children.
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Affiliation(s)
- Leila C Sahni
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - Eric A Naioti
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Samantha M Olson
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Angela P Campbell
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Marian G Michaels
- UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - John V Williams
- UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mary Allen Staat
- Department of Pediatrics, Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center Cincinnati, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Elizabeth P Schlaudecker
- Department of Pediatrics, Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center Cincinnati, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Monica M McNeal
- Department of Pediatrics, Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center Cincinnati, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Natasha B Halasa
- Vanderbilit University Medical Center, Nashville, Tennessee, USA
| | - Laura S Stewart
- Vanderbilit University Medical Center, Nashville, Tennessee, USA
| | - James D Chappell
- Vanderbilit University Medical Center, Nashville, Tennessee, USA
| | | | | | - Peter G Szilagyi
- University of California Los Angeles (UCLA) Mattel Children's Hospital, Los Angeles, California, USA
| | - Geoffrey A Weinberg
- University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Christopher J Harrison
- University of Missouri-Kansas City School of Medicine, Children's Mercy, Kansas City, Missouri, USA
| | - Rangaraj Selvarangan
- University of Missouri-Kansas City School of Medicine, Children's Mercy, Kansas City, Missouri, USA
| | - Jennifer E Schuster
- University of Missouri-Kansas City School of Medicine, Children's Mercy, Kansas City, Missouri, USA
| | - Parvin H Azimi
- University of California San Francisco (UCSF) Benioff Children's Hospital Oakland, Oakland, California, USA
| | - Monica N Singer
- University of California San Francisco (UCSF) Benioff Children's Hospital Oakland, Oakland, California, USA
| | - Vasanthi Avadhanula
- Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Pedro A Piedra
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Flor M Munoz
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
- Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Manish M Patel
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Julie A Boom
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
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13
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Hirotsu N, Sakaguchi H, Fukao K, Kojima S, Piedra PA, Tsuchiya K, Uehara T. Baloxavir safety and clinical and virologic outcomes in influenza virus-infected pediatric patients by age group: age-based pooled analysis of two pediatric studies conducted in Japan. BMC Pediatr 2023; 23:35. [PMID: 36681802 PMCID: PMC9860230 DOI: 10.1186/s12887-023-03841-5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/09/2023] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Anti-influenza treatment is important for children and is recommended in many countries. This study assessed safety, clinical, and virologic outcomes of baloxavir marboxil (baloxavir) treatment in children based on age and influenza virus type/subtype. METHODS This was a post hoc pooled analysis of two open-label non-controlled studies of a single weight-based oral dose of baloxavir (day 1) in influenza virus-infected Japanese patients aged < 6 years (n = 56) and ≥ 6 to < 12 years (n = 81). Safety, time to illness alleviation (TTIA), time to resolution of fever (TTRF), recurrence of influenza illness symptoms and fever (after day 4), virus titer, and outcomes by polymerase acidic protein variants at position I38 (PA/I38X) were evaluated. RESULTS Adverse events were reported in 39.0 and 39.5% of patients < 6 years and ≥ 6 to < 12 years, respectively. Median (95% confidence interval) TTIA was 43.2 (36.3-68.4) and 45.4 (38.9-61.0) hours, and TTRF was 32.2 (26.8-37.8) and 20.7 (19.2-23.8) hours, for patients < 6 years and ≥ 6 to < 12 years, respectively. Symptom and fever recurrence was more common in patients < 6 years with influenza B (54.5 and 50.0%, respectively) compared with older patients (0 and 25.0%, respectively). Virus titers declined (day 2) for both age groups. Transient virus titer increase and PA/I38X-variants were more common for patients < 6 years. CONCLUSIONS The safety and effectiveness of single-dose baloxavir were observed in children across all age groups and influenza virus types. Higher rates of fever recurrence and transient virus titer increase were observed in children < 6 years. TRIAL REGISTRATION Japan Pharmaceutical Information Center Clinical Trials Information JapicCTI-163,417 (registered 02 November 2016) and JapicCTI-173,811 (registered 15 December 2017).
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Affiliation(s)
| | | | - Keita Fukao
- Laboratory for Drug Discovery and Disease Research, Shionogi & Co., Ltd, Osaka, Japan
| | - Satoshi Kojima
- Medical Affairs Department, Shionogi & Co., Ltd, Osaka, Japan
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology and Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Kenji Tsuchiya
- Clinical Research Department, Shionogi & Co., Ltd, Osaka, Japan
| | - Takeki Uehara
- Drug Development and Regulatory Science Division, Shionogi & Co., Ltd, 8F, Nissay Yodoyabashi East, 3-3-13 Imabashi, Chuo-ku, Osaka, 541-0042, Japan.
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14
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Piedra FA, Henke D, Rajan A, Muzny DM, Doddapaneni H, Menon VK, Hoffman KL, Ross MC, Javornik Cregeen SJ, Metcalf G, Gibbs RA, Petrosino JF, Avadhanula V, Piedra PA. Modeling nonsegmented negative-strand RNA virus (NNSV) transcription with ejective polymerase collisions and biased diffusion. Front Mol Biosci 2023; 9:1095193. [PMID: 36699700 PMCID: PMC9868645 DOI: 10.3389/fmolb.2022.1095193] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
Infections by non-segmented negative-strand RNA viruses (NNSV) are widely thought to entail gradient gene expression from the well-established existence of a single promoter at the 3' end of the viral genome and the assumption of constant transcriptional attenuation between genes. But multiple recent studies show viral mRNA levels in infections by respiratory syncytial virus (RSV), a major human pathogen and member of NNSV, that are inconsistent with a simple gradient. Here we integrate known and newly predicted phenomena into a biophysically reasonable model of NNSV transcription. Our model succeeds in capturing published observations of respiratory syncytial virus and vesicular stomatitis virus (VSV) mRNA levels. We therefore propose a novel understanding of NNSV transcription based on the possibility of ejective polymerase-polymerase collisions and, in the case of RSV, biased polymerase diffusion.
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Affiliation(s)
- Felipe-Andrés Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States,*Correspondence: Felipe-Andrés Piedra,
| | - David Henke
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States
| | - Donna M. Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Unites States
| | - Harsha Doddapaneni
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Unites States
| | - Vipin K. Menon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Unites States
| | - Kristi L. Hoffman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States
| | - Matthew C. Ross
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Unites States
| | - Sara J. Javornik Cregeen
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States
| | - Ginger Metcalf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Unites States
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Unites States
| | - Joseph F. Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States,Department of Pediatrics, Baylor College of Medicine, Houston, TX, Unites States
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15
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Clark JR, Terwilliger A, Avadhanula V, Tisza M, Cormier J, Javornik-Cregeen S, Ross MC, Hoffman KL, Troisi C, Hanson B, Petrosino J, Balliew J, Piedra PA, Rios J, Deegan J, Bauer C, Wu F, Mena KD, Boerwinkle E, Maresso AW. Wastewater pandemic preparedness: Toward an end-to-end pathogen monitoring program. Front Public Health 2023; 11:1137881. [PMID: 37026145 PMCID: PMC10070845 DOI: 10.3389/fpubh.2023.1137881] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/09/2023] [Indexed: 04/08/2023] Open
Abstract
Molecular analysis of public wastewater has great potential as a harbinger for community health and health threats. Long-used to monitor the presence of enteric viruses, in particular polio, recent successes of wastewater as a reliable lead indicator for trends in SARS-CoV-2 levels and hospital admissions has generated optimism and emerging evidence that similar science can be applied to other pathogens of pandemic potential (PPPs), especially respiratory viruses and their variants of concern (VOC). However, there are substantial challenges associated with implementation of this ideal, namely that multiple and distinct fields of inquiry must be bridged and coordinated. These include engineering, molecular sciences, temporal-geospatial analytics, epidemiology and medical, and governmental and public health messaging, all of which present their own caveats. Here, we outline a framework for an integrated, state-wide, end-to-end human pathogen monitoring program using wastewater to track viral PPPs.
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Affiliation(s)
- Justin R. Clark
- TAILOR Labs, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Austen Terwilliger
- TAILOR Labs, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Michael Tisza
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Juwan Cormier
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Sara Javornik-Cregeen
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Matthew Clayton Ross
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Kristi Louise Hoffman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Catherine Troisi
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
| | - Blake Hanson
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
- Center for Infectious Diseases, Department of Epidemiology, Human Genetics and Environmental Sciences, Houston, TX, United States
| | - Joseph Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - John Balliew
- El Paso Water Utility, El Paso, TX, United States
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Pediatrics Department, Baylor College of Medicine, Houston, TX, United States
| | - Janelle Rios
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
| | - Jennifer Deegan
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
- The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Cici Bauer
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
- Department of Biostatistics and Data Science, UTHealth School of Public Health, Houston, TX, United States
| | - Fuqing Wu
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
| | - Kristina D. Mena
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
| | - Eric Boerwinkle
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, Houston, TX, United States
| | - Anthony W. Maresso
- TAILOR Labs, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Anthony W. Maresso
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16
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Chen J, Tan S, Avadhanula V, Moise L, Piedra PA, De Groot AS, Bahl J. Diversity and evolution of computationally predicted T cell epitopes against human respiratory syncytial virus. PLoS Comput Biol 2023; 19:e1010360. [PMID: 36626370 PMCID: PMC9870173 DOI: 10.1371/journal.pcbi.1010360] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 01/23/2023] [Accepted: 12/07/2022] [Indexed: 01/11/2023] Open
Abstract
Human respiratory syncytial virus (RSV) is a major cause of lower respiratory infection. Despite more than 60 years of research, there is no licensed vaccine. While B cell response is a major focus for vaccine design, the T cell epitope profile of RSV is also important for vaccine development. Here, we computationally predicted putative T cell epitopes in the Fusion protein (F) and Glycoprotein (G) of RSV wild circulating strains by predicting Major Histocompatibility Complex (MHC) class I and class II binding affinity. We limited our inferences to conserved epitopes in both F and G proteins that have been experimentally validated. We applied multidimensional scaling (MDS) to construct T cell epitope landscapes to investigate the diversity and evolution of T cell profiles across different RSV strains. We find the RSV strains are clustered into three RSV-A groups and two RSV-B groups on this T epitope landscape. These clusters represent divergent RSV strains with potentially different immunogenic profiles. In addition, our results show a greater proportion of F protein T cell epitope content conservation among recent epidemic strains, whereas the G protein T cell epitope content was decreased. Importantly, our results suggest that RSV-A and RSV-B have different patterns of epitope drift and replacement and that RSV-B vaccines may need more frequent updates. Our study provides a novel framework to study RSV T cell epitope evolution. Understanding the patterns of T cell epitope conservation and change may be valuable for vaccine design and assessment.
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Affiliation(s)
- Jiani Chen
- Center for Ecology of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
- Center for Influenza Disease and Emergence Response, University of Georgia, Athens, Georgia, United States of America
| | - Swan Tan
- Center for Ecology of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
- Center for Influenza Disease and Emergence Response, University of Georgia, Athens, Georgia, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Leonard Moise
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
- EpiVax Inc., Providence, Rhode Island, United States of America
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anne S. De Groot
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
- EpiVax Inc., Providence, Rhode Island, United States of America
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
- Center for Influenza Disease and Emergence Response, University of Georgia, Athens, Georgia, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, Georgia, United States of America
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17
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Keefe JA, Avadhanula V, Nicholson EG, Devaraj S, Piedra PA, Bozkurt B, Wehrens XH. Abnormalities in cardiac and inflammatory biomarkers in ambulatory subjects after COVID-19 infection. Int J Cardiol Heart Vasc 2022; 43:101144. [PMID: 36321063 PMCID: PMC9613792 DOI: 10.1016/j.ijcha.2022.101144] [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: 10/17/2022] [Revised: 10/22/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022]
Abstract
Background Coronavirus-2019 (COVID-19) is known to affect the heart and is associated with a pro-inflammatory state. Most studies to date have focused on clinically sick subjects. Here, we report cardiac and proinflammatory biomarkers levels in ambulatory young adults with asymptomatic or mild COVID-19 infection compared to those without infection 4-8 weeks after severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) testing. Methods 131 asymptomatic or mildly symptomatic subjects were enrolled following testing for SARS-COV-2. Fifty subjects tested negative, and 81 subjects tested positive. Serum samples were collected for measurement of C-reactive protein, ferritin, interleukin-6, NT-pro-B-type natriuretic peptide, and cardiac troponin 28-55 days after SARS-COV-2 RT-PCR testing. Results Biomarker levels trended higher in SARS-COV-2-positive vs negative subjects, but differences in biomarker levels or proportion of subjects with elevated biomarkers were not statistically significant with respect to SARS-COV-2 status. Among individuals with ≥ 1 comorbidity, odds of elevated CRP were greater compared to individuals without any comorbidities (odds ratio [OR] = 2.90); this effect size was increased 1.4-fold among SARS-COV-2-positive subjects (OR = 4.03). Similarly, NT-pro-BNP was associated with CVD, with the strongest association in COVID-positive individuals (OR = 16.9). Conclusions In a relatively young, healthy adult population, mild COVID-19 infection was associated with mild elevations in cardiac and proinflammatory biomarkers within 4-8 weeks of mild or asymptomatic COVID-19 infection in individuals with preexisting comorbidities, but not among individuals without comorbidities. For the general population of young adults, we did not find evidence of elevation of cardiac or proinflammatory biomarkers 4-8 weeks after COVID-19 infection.Clinical Perspective: This is a characterization of cardiac and proinflammatory biomarkers in ambulatory subjects following asymptomatic or mild COVID-19 infection. Young, ambulatory individuals did not have cardiac and proinflammatory biomarker elevation 4-8 weeks after mild COVID-19 infection. However, COVID-19 infection was associated with biomarker elevations in select individuals with comorbidities.Clinical study number: H-47423.
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Affiliation(s)
- Joshua A. Keefe
- Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX 77030, USA,Department of Integrative Physiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Vasanthi Avadhanula
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Erin G. Nicholson
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sridevi Devaraj
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Pedro A. Piedra
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Biykem Bozkurt
- Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX 77030, USA,Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA,Corresponding authors at: Cardiovascular Research Institute, Department of Medicine, Baylor College of Medicine, One Baylor Plaza, BCM620, USA (Biykem Bozkurt). Cardiovascular Research Institute, Department of Integrative Physiology, Baylor College of Medicine, One Baylor Plaza, BCM335 (Xander H.T. Wehrens)
| | - Xander H.T. Wehrens
- Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX 77030, USA,Department of Integrative Physiology, Baylor College of Medicine, Houston, TX 77030, USA,Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA,Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA,Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA,Center for Space Medicine, Baylor College of Medicine, Houston, TX 77030, USA,Corresponding authors at: Cardiovascular Research Institute, Department of Medicine, Baylor College of Medicine, One Baylor Plaza, BCM620, USA (Biykem Bozkurt). Cardiovascular Research Institute, Department of Integrative Physiology, Baylor College of Medicine, One Baylor Plaza, BCM335 (Xander H.T. Wehrens)
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18
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Banerjee D, Hassan F, Avadhanula V, Piedra PA, Boom J, Sahni LC, Weinberg GA, Lindstrom S, Rha B, Harrison CJ, Selvarangan R. Comparative analysis of three multiplex platforms for the detection of respiratory viral pathogens. J Clin Virol 2022; 156:105274. [PMID: 36099751 DOI: 10.1016/j.jcv.2022.105274] [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: 12/15/2021] [Revised: 08/24/2022] [Accepted: 08/27/2022] [Indexed: 10/31/2022]
Abstract
BACKGROUND Acute viral respiratory infections are a major health burden in children worldwide. In recent years, rapid and sensitive multiplex nucleic acid amplification tests (NAATs) have replaced conventional methods for routine virus detection in the clinical laboratory. OBJECTIVE/STUDY DESIGN We compared BioFire® FilmArray® Respiratory Panel (FilmArray V1.7), Luminex NxTag® Respiratory Pathogen Panel (NxTag RPP) and Applied Biosystems TaqMan Array Card (TAC) for the detection of eight viruses in pediatric respiratory specimens. Results from the three platforms were analyzed with a single-plex real-time RT-PCR (rRT-PCR) assay for each virus. RESULTS Of the 170/210 single-plex virus-positive samples, FilmArray detected a virus in 166 (97.6%), TAC in 163 (95.8%) and NxTag RPP in 160 (94.1%) samples. The Positive Percent Agreement (PPA) of FilmArray, NxTag RPP and TAC was highest for influenza B (100%, 100% and 95.2% respectively) and lowest for seasonal coronaviruses on both FilmArray (90.2%) and NxTag RPP (81.8%), and for parainfluenza viruses 1- 4 on TAC (84%). The Negative Percent Agreement (NPA) was lowest for rhinovirus/enterovirus (92.9%, 96.7% and 97.3%) on FilmArray, NxTag RPP and TAC respectively. NPA for all three platforms was highest (100%) for both parainfluenza viruses 1- 4 and influenza A and B, and 100% for human metapneumovirus with TAC as well. CONCLUSION All three multiplex platforms displayed high overall agreement (>90%) and high NPA (>90%), while PPA was pathogen dependent and varied among platforms; high PPA (>90%) was observed for FilmArray for all eight viruses, TAC for six viruses and NxTag RPP for 4 viruses.
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Affiliation(s)
- Dithi Banerjee
- Children's Mercy Hospital, Kansas City, MO, United States of America
| | - Ferdaus Hassan
- Children's Mercy Hospital, Kansas City, MO, United States of America
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America; Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States of America
| | - Julie Boom
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States of America; Texas Children's Hospital, Immunization Project, Baylor College of Medicine, Houston, TX, United States of America
| | - Leila C Sahni
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States of America; Texas Children's Hospital, Immunization Project, Baylor College of Medicine, Houston, TX, United States of America
| | - Geoffrey A Weinberg
- University of Rochester School of Medicine & Dentistry, Rochester, NY, United States of America
| | - Stephen Lindstrom
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Brian Rha
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
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19
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Probst V, Spieker AJ, Stopczynski T, Stewart LS, Haddadin Z, Selvarangan R, Harrison CJ, Schuster JE, Staat MA, McNeal M, Weinberg GA, Szilagyi PG, Boom JA, Sahni LC, Piedra PA, Englund JA, Klein EJ, Michaels MG, Williams JV, Campbell AP, Patel M, Gerber SI, Halasa NB. Clinical Presentation and Severity of Adenovirus Detection Alone vs Adenovirus Co-detection With Other Respiratory Viruses in US Children With Acute Respiratory Illness from 2016 to 2018. J Pediatric Infect Dis Soc 2022; 11:430-439. [PMID: 35849119 DOI: 10.1093/jpids/piac066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/28/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Human adenovirus (HAdV) is commonly associated with acute respiratory illnesses (ARI) in children and is also frequently co-detected with other viral pathogens. We compared clinical presentation and outcomes in young children with HAdV detected alone vs co-detected with other respiratory viruses. METHODS We used data from a multicenter, prospective, viral surveillance study of children seen in the emergency department and inpatient pediatric settings at seven US sites. Children less than 18 years old with fever and/or respiratory symptoms were enrolled between 12/1/16 and 10/31/18 and tested by molecular methods for HAdV, human rhinovirus/enterovirus (HRV/EV), respiratory syncytial virus (RSV), parainfluenza (PIV, types 1-4), influenza (flu, types A-C), and human metapneumovirus (HMPV). Our primary measure of illness severity was hospitalization; among hospitalized children, secondary severity outcomes included oxygen support and length of stay (LOS). RESULTS Of the 18,603 children enrolled, HAdV was detected in 1,136 (6.1%), among whom 646 (56.9%) had co-detection with at least one other respiratory virus. HRV/EV (n = 293, 45.3%) and RSV (n = 123, 19.0%) were the most frequent co-detections. Children with HRV/EV (aOR = 1.61; 95% CI = [1.11-2.34]), RSV (aOR = 4.48; 95% CI = [2.81-7.14]), HMPV (aOR = 3.39; 95% CI = [1.69-6.77]), or ≥ 2 co-detections (aOR = 1.95; 95% CI = [1.14-3.36]) had higher odds of hospitalization compared to children with HAdV alone. Among hospitalized children, HAdV co-detection with RSV or HMPV was each associated with higher odds of oxygen support, while co-detection with PIV or influenza viruses was each associated with higher mean LOS. CONCLUSIONS HAdV co-detection with other respiratory viruses was associated with greater disease severity among children with ARI compared to HAdV detection alone.
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Affiliation(s)
- Varvara Probst
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Andrew J Spieker
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Tess Stopczynski
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Laura S Stewart
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Zaid Haddadin
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Rangaraj Selvarangan
- Department of Pathology and Laboratory Medicine, University of Missouri-Kansas City and Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Christopher J Harrison
- Department of Pathology and Laboratory Medicine, University of Missouri-Kansas City and Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Jennifer E Schuster
- Department of Pediatrics, University of Missouri-Kansas City and Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Mary A Staat
- Department of Pediatrics, College of Medicine, University of Cincinnati and Division of Infectious Diseases, Cincinnati Children's Hospital, Cincinnati, Ohio, USA
| | - Monica McNeal
- Department of Pediatrics, College of Medicine, University of Cincinnati and Division of Infectious Diseases, Cincinnati Children's Hospital, Cincinnati, Ohio, USA
| | - Geoffrey A Weinberg
- Department of Pediatrics, School of Medicine and Dentistry, University of Rochester, Rochester, New York, USA
| | - Peter G Szilagyi
- Department of Pediatrics, School of Medicine and Dentistry, University of Rochester, Rochester, New York, USA
- Department of Pediatrics, University of California at Los Angeles Mattel Children's Hospital and University of California at Los Angeles, Los Angeles, California, USA
| | - Julie A Boom
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, Texas Children's Hospital, Houston, Texas, USA
| | - Leila C Sahni
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, Texas Children's Hospital, Houston, Texas, USA
| | - Pedro A Piedra
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, Texas Children's Hospital, Houston, Texas, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas. Texas Children's Hospital, Houston, Texas, USA
| | - Janet A Englund
- Department of Pediatrics, University of Washington School of Medicine and Seattle Children's Hospital, Seattle, Washington, USA
| | - Eileen J Klein
- Department of Pediatrics, University of Washington School of Medicine and Seattle Children's Hospital, Seattle, Washington, USA
| | - Marian G Michaels
- Department of Pediatrics, School of Medicine, University of Pittsburgh and University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John V Williams
- Department of Pediatrics, School of Medicine, University of Pittsburgh and University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Angela P Campbell
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Manish Patel
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Susan I Gerber
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Natasha B Halasa
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Vanderbilt University, Nashville, Tennessee, USA
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20
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Fujiogi M, Raita Y, Pérez-Losada M, Freishtat RJ, Celedón JC, Mansbach JM, Piedra PA, Zhu Z, Camargo CA, Hasegawa K. Integrated relationship of nasopharyngeal airway host response and microbiome associates with bronchiolitis severity. Nat Commun 2022; 13:4970. [PMID: 36042194 PMCID: PMC9427849 DOI: 10.1038/s41467-022-32323-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 11/22/2021] [Accepted: 07/25/2022] [Indexed: 12/03/2022] Open
Abstract
Bronchiolitis is a leading cause of infant hospitalizations but its immunopathology remains poorly understood. Here we present data from 244 infants hospitalized with bronchiolitis in a multicenter prospective study, assessing the host response (transcriptome), microbial composition, and microbial function (metatranscriptome) in the nasopharyngeal airway, and associate them with disease severity. We investigate individual associations with disease severity identify host response, microbial taxonomical, and microbial functional modules by network analyses. We also determine the integrated relationship of these modules with severity. Several modules are significantly associated with risks of positive pressure ventilation use, including the host-type I interferon, neutrophil/interleukin-1, T cell regulation, microbial-branched-chain amino acid metabolism, and nicotinamide adenine dinucleotide hydrogen modules. Taken together, we show complex interplays between host and microbiome, and their contribution to disease severity. Bronchiolitis is major cause of infection, morbidity and hospitalisation. Here the authors apply transcriptomic based assessment of the host response, microbiome composition and function, and associate this to bronchiolitis severity.
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Affiliation(s)
- Michimasa Fujiogi
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Yoshihiko Raita
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Marcos Pérez-Losada
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, The George Washington University, Washington, DC, USA.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Robert J Freishtat
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA.,Division of Emergency Medicine, Children's National Hospital, Washington, DC, USA.,Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Juan C Celedón
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jonathan M Mansbach
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Pedro A Piedra
- Departments of Molecular Virology and Microbiology and Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Zhaozhong Zhu
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Carlos A Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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21
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Blunck BN, Angelo LS, Henke D, Avadhanula V, Cusick M, Ferlic-Stark L, Zechiedrich L, Gilbert BE, Piedra PA. Adult Memory T Cell Responses to the Respiratory Syncytial Virus Fusion Protein During a Single RSV Season (2018-2019). Front Immunol 2022; 13:823652. [PMID: 35422803 PMCID: PMC9002099 DOI: 10.3389/fimmu.2022.823652] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 03/02/2022] [Indexed: 11/13/2022] Open
Abstract
Respiratory Syncytial Virus (RSV) is ubiquitous and re-infection with both subtypes (RSV/A and RSV/B) is common. The fusion (F) protein of RSV is antigenically conserved, induces neutralizing antibodies, and is a primary target of vaccine development. Insight into the breadth and durability of RSV-specific adaptive immune response, particularly to the F protein, may shed light on susceptibility to re-infection. We prospectively enrolled healthy adult subjects (n = 19) and collected serum and peripheral blood mononuclear cells (PBMCs) during the 2018–2019 RSV season. Previously, we described their RSV-specific antibody responses and identified three distinct antibody kinetic profiles associated with infection status: uninfected (n = 12), acutely infected (n = 4), and recently infected (n = 3). In this study, we measured the longevity of RSV-specific memory T cell responses to the F protein following natural RSV infection. We stimulated PBMCs with overlapping 15-mer peptide libraries spanning the F protein derived from either RSV/A or RSV/B and found that memory T cell responses mimic the antibody responses for all three groups. The uninfected group had stable, robust memory T cell responses and polyfunctionality. The acutely infected group had reduced polyfunctionality of memory T cell response at enrollment compared to the uninfected group, but these returned to comparable levels by end-of-season. The recently infected group, who were unable to maintain high levels of RSV-specific antibody following infection, similarly had decreased memory T cell responses and polyfunctionality during the RSV season. We observed subtype-specific differences in memory T cell responses and polyfunctionality, with RSV/A stimulating stronger memory T cell responses with higher polyfunctionality even though RSV/B was the dominant subtype in circulation. A subset of individuals demonstrated an overall deficiency in the generation of a durable RSV-specific adaptive immune response. Because memory T cell polyfunctionality may be associated with protection against re-infection, this latter group would likely be at greater risk of re-infection. Overall, these results expand our understanding of the longevity of the adaptive immune response to the RSV fusion protein and should be considered in future vaccine development efforts.
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Affiliation(s)
- Brittani N Blunck
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Laura S Angelo
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - David Henke
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Matthew Cusick
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Laura Ferlic-Stark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Lynn Zechiedrich
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States.,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, United States
| | - Brian E Gilbert
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
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22
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Dumas O, Erkkola R, Bergroth E, Hasegawa K, Mansbach JM, Piedra PA, Jartti T, Camargo CA. Severe bronchiolitis profiles and risk of asthma development in Finnish children. J Allergy Clin Immunol 2022; 149:1281-1285.e1. [PMID: 34624392 DOI: 10.1016/j.jaci.2021.08.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 08/02/2021] [Accepted: 08/26/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND Recent studies support the existence of several entities under the clinical diagnosis of bronchiolitis. Among infants with severe bronchiolitis, distinct profiles have been differentially associated with development of recurrent wheezing by age 3 years. However, their associations with actual asthma remain unclear. OBJECTIVE Our aim was to study the association between severe bronchiolitis profiles identified by using a clustering approach and childhood asthma. METHODS Among 408 children (aged <2 years) hospitalized with bronchiolitis in Finland (in 2008-2010), latent class analysis identified 3 bronchiolitis profiles: profile A (47%), characterized by history of wheezing and/or eczema, wheezing during acute illness, and rhinovirus infection; profile BC (38%), characterized by severe illness and respiratory syncytial virus infection; and profile D (15%), characterized by the least severely ill children, including mostly children without wheezing and with rhinovirus infection. The children were followed by questionnaire 4 years later (86% [n = 348]) and through a nationwide social insurance database 7 years later (99% [n = 403]). Current asthma at the 4- and 7-year follow-ups was defined by regular use (according to parental report and medical records) or purchase (according to the social insurance database) of asthma control medication. RESULTS Compared with risk of current asthma associated with profile BC, we observed increased risk of current asthma associated with profile A both at the 4-year follow-up (age- and sex-adjusted odds ratio = 2.42 [95% CI = 1.23-4.75]) and at the 7-year follow-up (age- and sex-adjusted odds ratio = 3.14 [95% CI = 1.33-7.42]). No significant difference in asthma risk was observed between profile D and profile BC. CONCLUSION These longitudinal results provide further support for an association between a distinct severe bronchiolitis profile (characterized by a history of wheezing and/or eczema and rhinovirus infection) and risk of development childhood asthma.
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Affiliation(s)
- Orianne Dumas
- Université Paris-Saclay, UVSQ, Inserm, CESP, Equipe d'Epidémiologie Respiratoire Intégrative, 94807, Villejuif, France.
| | - Riku Erkkola
- Department of Children and Adolescents, Turku University Hospital and University of Turku, Turku, Finland
| | - Eija Bergroth
- Department of Pediatrics, Kuopio University Hospital, Kuopio, Finland; Department of Pediatrics, Central Hospital of Central Finland, Jyväskylä, Finland
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Mass
| | - Jonathan M Mansbach
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Mass
| | - Pedro A Piedra
- Departments of Molecular Virology and Microbiology and Pediatrics, Baylor College of Medicine, Houston, Tex
| | - Tuomas Jartti
- Department of Children and Adolescents, Turku University Hospital and University of Turku, Turku, Finland; PEDEGO Research Unit, Medical Research Center, University of Oulu, Oulu, Finland; Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Carlos A Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Mass
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23
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Blunck BN, Aideyan L, Ye X, Avadhanula V, Ferlic-Stark L, Zechiedrich L, Gilbert BE, Piedra PA. Antibody responses of healthy adults to the p27 peptide of respiratory syncytial virus fusion protein. Vaccine 2022; 40:536-543. [PMID: 34903371 PMCID: PMC8755595 DOI: 10.1016/j.vaccine.2021.11.087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 03/22/2021] [Revised: 11/13/2021] [Accepted: 11/28/2021] [Indexed: 01/26/2023]
Abstract
The respiratory syncytial virus (RSV) fusion (F) protein undergoes two furin-cleavage events to become fusion competent, resulting in the release of a twenty-seven amino acid peptide (p27). Recent studies indicate that the p27 region of the F protein was an immunodominant antigen in young children. In this study, we evaluated the kinetics of the serum antibody response to the p27 peptide following natural RSV reinfection in adults. Nineteen healthy adults under sixty-five years of age were enrolled during the 2018-2019 RSV season in Houston, TX. Blood was collected at three study visits and RSV infection status was defined by changes in neutralizing antibody resulting in three groups: uninfected (n = 12), acutely infected (n = 4), and recently infected (n = 3). Serum IgG and IgA antibodies against RSV/A and RSV/B p27 peptides were measured by enzyme-linked immunosorbent assays, and serum p27-like antibodies were detected by a p27 competitive antibody assay. Anti-p27 antibodies were detected in all subjects at each study visit. The measured IgG and IgA anti-p27 antibody levels followed the same pattern as other RSV site-specific and neutralizing antibody responses described for this cohort previously: the uninfected group had stable responses for the duration of the study period, the acutely infected group had a significant increase following RSV infection, and the recently infected group had a decrease in anti-p27 antibody during the study period. These results indicate that antibodies to the p27 region of the F protein are generated following natural RSV reinfection and suggest that some of the F protein is potentially in a partially cleaved state on the surface of virions, expanding on the previous assumption that all of p27 is post-translationally released and not present on mature F. Additionally, antibody responses were significantly lower (1.4-1.5-fold) toward RSV/B than to RSV/A p27 at each study visit, despite being an RSV/B dominant outbreak. Understanding the mechanism for the differences in the magnitude of the RSV/A and RSV/B p27 antibody response may enhance our understanding of the intracellular processing of the F protein.
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Affiliation(s)
- Brittani N. Blunck
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Letisha Aideyan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Xunyan Ye
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Laura Ferlic-Stark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Lynn Zechiedrich
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX USA,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX USA
| | - Brian E. Gilbert
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA,Department of Pediatrics, Baylor College of Medicine, Houston, TX USA,Corresponding Author: Pedro A. Piedra,
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24
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Chen J, Qiu X, Avadhanula V, Shepard SS, Kim DK, Hixson J, Piedra PA, Bahl J. Novel and extendable genotyping system for human respiratory syncytial virus based on whole-genome sequence analysis. Influenza Other Respir Viruses 2021; 16:492-500. [PMID: 34894077 PMCID: PMC8983899 DOI: 10.1111/irv.12936] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 05/05/2021] [Revised: 09/12/2021] [Accepted: 10/17/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Human respiratory syncytial virus (RSV) is one of the leading causes of respiratory infections, especially in infants and young children. Previous RSV sequencing studies have primarily focused on partial sequencing of G gene (200-300 nucleotides) for genotype characterization or diagnostics. However, the genotype assignment with G gene has not recapitulated the phylogenetic signal of other genes, and there is no consensus on RSV genotype definition. METHODS We conducted maximum likelihood phylogenetic analysis with 10 RSV individual genes and whole-genome sequence (WGS) that are published in GenBank. RSV genotypes were determined by using phylogenetic analysis and pair-wise node distances. RESULTS In this study, we first statistically examined the phylogenetic incongruence, rate variation for each RSV gene sequence and WGS. We then proposed a new RSV genotyping system based on a comparative analysis of WGS and the temporal distribution of strains. We also provide an RSV classification tool to perform RSV genotype assignment and a publicly accessible up-to-date instance of Nextstrain where the phylogenetic relationship of all genotypes can be explored. CONCLUSIONS This revised RSV genotyping system will provide important information for disease surveillance, epidemiology, and vaccine development.
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Affiliation(s)
- Jiani Chen
- Center for Ecology of Infectious Diseases, Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Xueting Qiu
- Department of Infectious Disease, University of Georgia, Athens, GA, USA.,Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Vasanthi Avadhanula
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Samuel S Shepard
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Do-Kyun Kim
- Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, University of Texas Health Science Center, Houston, TX, USA
| | - James Hixson
- Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, University of Texas Health Science Center, Houston, TX, USA
| | - Pedro A Piedra
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Institute of Bioinformatics, University of Georgia, Athens, GA, USA.,Department of Infectious Disease, University of Georgia, Athens, GA, USA.,Department of Epidemiology and Biostatistics, University of Georgia, Athens, GA, USA
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25
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Ye X, Angelo LS, Nicholson EG, Iwuchukwu OP, Cabral de Rezende W, Rajan A, Aideyan LO, McBride TJ, Bond N, Santarcangelo P, Rayford YJ, Ferlic-Stark L, Fragoso S, Momin Z, Liu H, Truong K, Lopez B, Conner ME, Rice AP, Kimata JT, Avadhanula V, Piedra PA. Serum IgG anti-SARS-CoV-2 Binding Antibody Level Is Strongly Associated With IgA and Functional Antibody Levels in Adults Infected With SARS-CoV-2. Front Immunol 2021; 12:693462. [PMID: 34691016 PMCID: PMC8531527 DOI: 10.3389/fimmu.2021.693462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 04/11/2021] [Accepted: 09/20/2021] [Indexed: 12/24/2022] Open
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in December 2019 in Wuhan, China, and then rapidly spread causing an unprecedented pandemic. A robust serological assay is needed to evaluate vaccine candidates and better understand the epidemiology of coronavirus disease (COVID-19). Methods We used the full-length spike (S) protein of SARS-CoV-2 for the development of qualitative and quantitative IgG and IgA anti-S enzyme linked immunosorbent assays (ELISA). A total of 320 sera used for assay development were comprised of pandemic sera from SARS-CoV-2 infected adults (n=51) and pre-pandemic sera (n=269) including sera from endemic human coronavirus infected adults. Reverse cumulative curves and diagnostic test statistics were evaluated to define the optimal serum dilution and OD cutoff value for IgG anti-S and IgA anti-S ELISAs. The IgG and IgA anti-S, and three functional antibodies (ACE-2 receptor blocking antibody, lentipseudovirus-S neutralizing antibody, and SARS-CoV-2 neutralizing antibody) were measured using additional SARS-CoV-2 PCR positive sera (n=76) and surveillance sera (n=25). Lastly, the IgG and IgA anti-S levels were compared in different demographic groups. Results The optimal serum dilution for the qualitative IgG anti-S ELISA was at 1:1024 yielding a 99.6% specificity, 92.2% sensitivity, 92.9% positive predictive value (PPV), and 99.6% negative predictive value (NPV) at a SARS-CoV-2 seroprevalence of 5%. The optimal serum dilution for the qualitative IgA anti-S ELISA was at 1:128 yielding a 98.9% specificity, 76.5% sensitivity, 78.3% PPV, and 98.8% NPV at the same seroprevalence. Significant correlations were demonstrated between the IgG and IgA (r=0.833 for concentrations, r=0.840 for titers) as well as between IgG and three functional antibodies (r=0.811-0.924 for concentrations, r=0.795-0.917 for titers). The IgG and IgA anti-S levels were significantly higher in males than females (p<0.05), and in adults with moderate/severe symptoms than in adults with mild/moderate symptoms (p<0.001). Conclusion We developed a highly specific and sensitive IgG anti-S ELISA assay to SARS-CoV-2 using full length S protein. The IgG anti-S antibody level was strongly associated with IgA and functional antibody levels in adults with SARS-CoV-2 infection. Gender and disease severity, rather than age, play an important role in antibody levels.
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Affiliation(s)
- Xunyan Ye
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Laura S Angelo
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Erin G Nicholson
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Obinna P Iwuchukwu
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Wanderson Cabral de Rezende
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States.,Department of Pharmacology, Baylor College of Medicine, Houston, TX, United States
| | - Anubama Rajan
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Letisha O Aideyan
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Trevor J McBride
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Nanette Bond
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Patricia Santarcangelo
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Yolanda J Rayford
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Laura Ferlic-Stark
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Sonia Fragoso
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Zoha Momin
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Hongbing Liu
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Khanghy Truong
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Brianna Lopez
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Margaret E Conner
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Andrew P Rice
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Jason T Kimata
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Vasanthi Avadhanula
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Pedro A Piedra
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States.,Department of Pharmacology, Baylor College of Medicine, Houston, TX, United States.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
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26
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Farinholt T, Doddapaneni H, Qin X, Menon V, Meng Q, Metcalf G, Chao H, Gingras MC, Avadhanula V, Farinholt P, Agrawal C, Muzny DM, Piedra PA, Gibbs RA, Petrosino J. Transmission event of SARS-CoV-2 delta variant reveals multiple vaccine breakthrough infections. BMC Med 2021; 19:255. [PMID: 34593004 PMCID: PMC8483940 DOI: 10.1186/s12916-021-02103-4] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/18/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND This study aims to identify the causative strain of SARS-CoV-2 in a cluster of vaccine breakthroughs. Vaccine breakthrough by a highly transmissible SARS-CoV-2 strain is a risk to global public health. METHODS Nasopharyngeal swabs from suspected vaccine breakthrough cases were tested for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) by qPCR (quantitative polymerase chain reaction) for Wuhan-Hu1 and alpha variant. Positive samples were then sequenced by Swift Normalase Amplicon Panels to determine the causal variant. GATK (genome analysis toolkit) variants were filtered with allele fraction ≥80 and min read depth 30x. RESULTS Viral sequencing revealed an infection cluster of 6 vaccinated patients infected with the delta (B.1.617.2) SARS-CoV-2 variant. With no history of vaccine breakthrough, this suggests the delta variant may possess immune evasion in patients that received the Pfizer BNT162b2, Moderna mRNA-1273, and Covaxin BBV152. CONCLUSIONS Delta variant may pose the highest risk out of any currently circulating SARS-CoV-2 variants, with previously described increased transmissibility over alpha variant and now, possible vaccine breakthrough. FUNDING Parts of this work was supported by the National Institute of Allergy and Infectious Diseases (1U19AI144297) and Baylor College of Medicine internal funding.
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Affiliation(s)
- Timothy Farinholt
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
| | - Harsha Doddapaneni
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Xiang Qin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Vipin Menon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Qingchang Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ginger Metcalf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Hsu Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Marie-Claude Gingras
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Vasanthi Avadhanula
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Paige Farinholt
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Charu Agrawal
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Pedro A Piedra
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Joseph Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
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27
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Sahni LC, Avadhanula V, Ortiz CS, Feliz KE, John RE, Brown CA, Lively JY, Rha B, Munoz FM, Piedra PA, Dunn JJ, Boom JA. Comparison of Mid-Turbinate and Nasopharyngeal Specimens for Molecular Detection of SARS-CoV-2 Among Symptomatic Outpatients at a Pediatric Drive-Through Testing Site. J Pediatric Infect Dis Soc 2021; 10:872-879. [PMID: 34173660 DOI: 10.1093/jpids/piab046] [Citation(s) in RCA: 3] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/27/2021] [Indexed: 11/14/2022]
Abstract
BACKGROUND Nasopharyngeal (NP) specimen testing by reverse transcriptase polymerase chain reaction (RT-PCR) is the standard of care for detecting SARS-CoV-2. Data comparing the sensitivity and specificity of the NP specimen to the less invasive, mid-turbinate (MT) nasal specimen in children are limited. METHODS Paired clinical NP and research MT specimens were collected from children <18 years with respiratory symptoms and tested by molecular assays to detect SARS-CoV-2 RNA. Sensitivity, specificity, and agreement (Cohen's kappa [κ]) were calculated for research MT specimens compared to the clinical NP specimens. RESULTS Out of 907 children, 569 (62.7%) had parental consent and child assent when appropriate to participate and provided paired MT and NP specimens a median of 4 days after symptom onset (range 1-14 days). 16.5% (n = 94) of MT specimens were positive for SARS-CoV-2 compared with 20.0% (n = 114) of NP specimens. The sensitivity of research MT compared to clinical NP specimens was 82.5% (95% CI: 74.2%, 88.9%), specificity was 100.0% (95% CI: 99.2%, 100.0%), and overall agreement was 96.1% (κ = 0.87). The sensitivity of MT specimens decreased with time from 100% (95% CI: 59.0%, 100.0%) on day 1 of illness to 82.1% (95% CI: 73.8%, 88.7%) within 14 days of illness onset; sensitivity was generally >90% when specimens were collected within the first week of illness. CONCLUSION MT specimens, particularly those collected within the first week of illness, have moderately reduced sensitivity and equivalent specificity to less-tolerated NP specimens in pediatric outpatients. MT specimen use in children may represent a viable alternative to NP specimen collection.
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Affiliation(s)
- Leila C Sahni
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Immunization Project, Texas Children's Hospital, Houston, Texas, USA
| | - Vasanthi Avadhanula
- Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Camerin S Ortiz
- Immunization Project, Texas Children's Hospital, Houston, Texas, USA
| | - Karen E Feliz
- Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Rebekah E John
- Immunization Project, Texas Children's Hospital, Houston, Texas, USA
| | - Cameron A Brown
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA
| | - Joana Y Lively
- Centers for Disease Control and Prevention COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,IHRC, Inc., Atlanta, Georgia, USA
| | - Brian Rha
- Centers for Disease Control and Prevention COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Flor M Munoz
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Pedro A Piedra
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - James J Dunn
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA
| | - Julie A Boom
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Immunization Project, Texas Children's Hospital, Houston, Texas, USA
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28
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Avadhanula V, Piedra PA. The Prevention of Common Respiratory Virus Epidemics in 2020-21 during the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Pandemic: An Unexpected Benefit of the Implementation of Public Health Measures. Lancet Reg Health Am 2021; 2:100043. [PMID: 34430955 PMCID: PMC8377442 DOI: 10.1016/j.lana.2021.100043] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/03/2022]
Affiliation(s)
- Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, US
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29
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Doddapaneni H, Cregeen SJ, Sucgang R, Meng Q, Qin X, Avadhanula V, Chao H, Menon V, Nicholson E, Henke D, Piedra FA, Rajan A, Momin Z, Kottapalli K, Hoffman KL, Sedlazeck FJ, Metcalf G, Piedra PA, Muzny DM, Petrosino JF, Gibbs RA. Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals. PLoS One 2021; 16:e0244468. [PMID: 34432798 PMCID: PMC8386831 DOI: 10.1371/journal.pone.0244468] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 08/09/2021] [Indexed: 02/06/2023] Open
Abstract
The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity among samples. Mixed allelic frequencies along the 20kb ORF1ab gene in one sample, suggested the presence of a defective viral RNA species subpopulation maintained in mixture with functional RNA in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.
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Affiliation(s)
- Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sara Javornik Cregeen
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard Sucgang
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Hsu Chao
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Vipin Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Erin Nicholson
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - David Henke
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Felipe-Andres Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Zeineen Momin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kavya Kottapalli
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kristi L. Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph F. Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
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30
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Rajan A, Weaver AM, Aloisio GM, Jelinski J, Johnson HL, Venable SF, McBride T, Aideyan L, Piedra FA, Ye X, Melicoff-Portillo E, Yerramilli MRK, Zeng XL, Mancini MA, Stossi F, Maresso AW, Kotkar SA, Estes MK, Blutt S, Avadhanula V, Piedra PA. The human nose organoid respiratory virus model: an ex-vivo human challenge model to study RSV and SARS-CoV-2 pathogenesis and evaluate therapeutics. bioRxiv 2021. [PMID: 34341793 DOI: 10.1101/2021.07.28.453844] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
There is an unmet need for pre-clinical models to understand the pathogenesis of human respiratory viruses; and predict responsiveness to immunotherapies. Airway organoids can serve as an ex-vivo human airway model to study respiratory viral pathogenesis; however, they rely on invasive techniques to obtain patient samples. Here, we report a non-invasive technique to generate human nose organoids (HNOs) as an alternate to biopsy derived organoids. We made air liquid interface (ALI) cultures from HNOs and assessed infection with two major human respiratory viruses, respiratory syncytial virus (RSV) and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Infected HNO-ALI cultures recapitulate aspects of RSV and SARS-CoV-2 infection, including viral shedding, ciliary damage, innate immune responses, and mucus hyper-secretion. Next, we evaluated the feasibility of the HNO-ALI respiratory virus model system to test the efficacy of palivizumab to prevent RSV infection. Palivizumab was administered in the basolateral compartment (circulation) while viral infection occurred in the apical ciliated cells (airways), simulating the events in infants. In our model, palivizumab effectively prevented RSV infection in a concentration dependent manner. Thus, the HNO-ALI model can serve as an alternate to lung organoids to study respiratory viruses and testing therapeutics.
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31
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Farinholt T, Doddapaneni H, Qin X, Menon V, Meng Q, Metcalf G, Chao H, Gingras MC, Farinholt P, Agrawal C, Muzny DM, Piedra PA, Gibbs RA, Petrosino J. Transmission event of SARS-CoV-2 Delta variant reveals multiple vaccine breakthrough infections. medRxiv 2021:2021.06.28.21258780. [PMID: 34268529 PMCID: PMC8282118 DOI: 10.1101/2021.06.28.21258780] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Importance Vaccine breakthrough by an emergent SARS-CoV-2 variant poses a great risk to global public health. Objective To determine the SARS-CoV-2 variant responsible for 6 cases of vaccine breakthrough. Design Nasopharyngeal swabs from suspected vaccine breakthrough cases were tested for SARS-CoV-2 by qPCR for Wuhan-Hu1 and Alpha variant. Positive samples were then sequenced by Swift Normalase Amplicon Panels to determine the causal variant. Setting Transmission event occurred at events surrounding a wedding outside of Houston, TX. Two patients from India, likely transmitted the Delta variant to other guests. Participants Following a positive SARS-CoV-2 qPCR test at a third-party site, six fully vaccinated patients were investigated. Three males and three females ranged from 53 to 69 years old. One patient suffered from diabetes while three others were classified as overweight. No significant other comorbidities were identified. None of the patients had a history of failed vaccination.
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Affiliation(s)
- Timothy Farinholt
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Harsha Doddapaneni
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Xiang Qin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Vipin Menon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Qingchang Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ginger Metcalf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Hsu Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Marie-Claude Gingras
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Paige Farinholt
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Charu Agrawal
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Pedro A Piedra
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Joseph Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
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32
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Hayden FG, Asher J, Cowling BJ, Hurt AC, Ikematsu H, Kuhlbusch K, Lemenuel-Diot A, Du Z, Meyers LA, Piedra PA, Takazono T, Yen HL, Monto AS. Reducing influenza virus transmission: the value of antiviral treatment. Clin Infect Dis 2021; 74:532-540. [PMID: 34245250 PMCID: PMC8834654 DOI: 10.1093/cid/ciab625] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 04/30/2021] [Indexed: 11/16/2022] Open
Abstract
Prompt antiviral treatment has the potential to reduce influenza virus transmission to close contacts, but rigorous data on the magnitude of treatment effects on transmission are limited. Animal model data indicate that rapid reductions in viral replication after antiviral treatment reduce the risk of transmission. Observational and clinical trial data with oseltamivir and other neuraminidase inhibitors indicate that prompt treatment of household index patients seems to reduce the risk of illness in contacts, although the magnitude of the reported effects has varied widely across studies. In addition, the potential risk of transmitting drug-resistant variants exists with all approved classes of influenza antivirals. A controlled trial examining baloxavir treatment efficacy to reduce transmission, including the risk of transmitting virus with reduced baloxavir susceptibility, is currently in progress. If reduced transmission risk is confirmed, modeling studies indicate that early treatment could have major epidemiologic benefits in seasonal and pandemic influenza.
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Affiliation(s)
- Frederick G Hayden
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, USA
| | | | - Benjamin J Cowling
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | | | | | | | | | - Zhanwei Du
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Lauren Ancel Meyers
- Department of Integrative Biology and Statistics & Data Sciences, University of Texas, Austin, Texas, USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, USA
| | - Takahiro Takazono
- Department of Infectious Diseases, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hui-Ling Yen
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Arnold S Monto
- University of Michigan School of Public Health, Ann Arbor, Michigan, USA
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33
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Salimi V, Viegas M, Trento A, Agoti CN, Anderson LJ, Avadhanula V, Bahl J, Bont L, Brister JR, Cane PA, Galiano M, Graham BS, Hatcher EL, Hellferscee O, Henke DM, Hirve S, Jackson S, Keyaerts E, Kragten-Tabatabaie L, Lindstrom S, Nauwelaers I, Nokes DJ, Openshaw PJ, Peret TC, Piedra PA, Ramaekers K, Rector A, Trovão NS, von Gottberg A, Zambon M, Zhang W, Williams TC, Barr IG, Buchholz UJ. Proposal for Human Respiratory Syncytial Virus Nomenclature below the Species Level. Emerg Infect Dis 2021; 27:1-9. [PMID: 34013862 PMCID: PMC8153853 DOI: 10.3201/eid2706.204608] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Human respiratory syncytial virus (HRSV) is the leading viral cause of serious pediatric respiratory disease, and lifelong reinfections are common. Its 2 major subgroups, A and B, exhibit some antigenic variability, enabling HRSV to circulate annually. Globally, research has increased the number of HRSV genomic sequences available. To ensure accurate molecular epidemiology analyses, we propose a uniform nomenclature for HRSV-positive samples and isolates, and HRSV sequences, namely: HRSV/subgroup identifier/geographic identifier/unique sequence identifier/year of sampling. We also propose a template for submitting associated metadata. Universal nomenclature would help researchers retrieve and analyze sequence data to better understand the evolution of this virus.
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34
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Ivanov V, Oomens AGP, Papin JF, Staats R, Reuter DN, Yu Z, Piedra PA, Wellliver RC. Intranasal and intrapulmonary vaccination with an M protein-deficient respiratory syncytial virus (RSV) vaccine improves clinical signs and reduces viral replication in infant baboons after an RSV challenge infection. Vaccine 2021; 39:4063-4071. [PMID: 34140172 DOI: 10.1016/j.vaccine.2021.06.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/23/2021] [Accepted: 06/04/2021] [Indexed: 11/17/2022]
Abstract
Respiratory syncytial virus (RSV) is the major viral respiratory pathogen for human infants and children. Despite a severe global burden incurred by annual RSV epidemics, there is no licensed RSV vaccine. We have developed an RSV vaccine from a human RSV strain from which the gene for the viral M protein has been deleted ("Mnull RSV"). RSV infects airway cells and produces each of its proteins. The M protein is responsible for reassembling the various other synthesized viral proteins into new, intact virus. In the absence of the M protein, therefore, reassembly does not occur, and the Mnull RSV does not replicate. We vaccinated 2-week old infant baboons with Mnull RSV either intranasally (IN) or directly into the lung (intratracheal, or IT), then infected these animals by inoculating human RSV directly into the lung. IN vaccination induced inconsistent serum RSV neutralizing antibody (NA) responses, but provided moderate reductions in respiratory rates, overall signs of illness and viral replication in bronchoalveolar lavage (BAL) fluid following infection. Intratracheal vaccination induced much stronger RSV NA responses, which persisted for at least 4-6 months. Following RSV infection, animals vaccinated by the IT route had much greater reductions in tachypnea and work of breathing than animals vaccinated IN, and had undetectable amounts of virus in BAL fluids. These results support the further development of IT Mnull RSV vaccination to reduce the impact of RSV infection in humans.
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Affiliation(s)
- Vadim Ivanov
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, 1100 North Lindsay Ave., Oklahoma City, OK 73104, USA.
| | - Antonius G P Oomens
- Department of Veterinary Pathology, College of Veterinary Medicine, Room 258 McElroy Hall, Oklahoma State University, Stillwater, OK 74074, USA.
| | - James F Papin
- Division of Comparative Medicine, The University of Oklahoma, Health Sciences Center, 940 Stanton L. Young Blvd., Oklahoma City, OK 73104, USA.
| | - Rachel Staats
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, 1100 North Lindsay Ave., Oklahoma City, OK 73104, USA.
| | - Darlene N Reuter
- Division of Comparative Medicine, The University of Oklahoma, Health Sciences Center, 940 Stanton L. Young Blvd., Oklahoma City, OK 73104, USA.
| | - Zhongxin Yu
- Department of Pathology, College of Medicine, University of Oklahoma Health Sciences Center, 1100 North Lindsay Ave., Oklahoma City, OK 73104, USA.
| | - Pedro A Piedra
- Department of Molecular Biology and Microbiology and Pediatrics, Baylor College of Medicine, Baylor University, 1 Baylor Plaza, Houston, TX 77030, USA.
| | - Robert C Wellliver
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, 1100 North Lindsay Ave., Oklahoma City, OK 73104, USA.
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35
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Raita Y, Pérez-Losada M, Freishtat RJ, Harmon B, Mansbach JM, Piedra PA, Zhu Z, Camargo CA, Hasegawa K. Integrated omics endotyping of infants with respiratory syncytial virus bronchiolitis and risk of childhood asthma. Nat Commun 2021; 12:3601. [PMID: 34127671 PMCID: PMC8203688 DOI: 10.1038/s41467-021-23859-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [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: 12/08/2020] [Accepted: 05/17/2021] [Indexed: 02/04/2023] Open
Abstract
Respiratory syncytial virus (RSV) bronchiolitis is not only the leading cause of hospitalization in U.S. infants, but also a major risk factor for asthma development. While emerging evidence suggests clinical heterogeneity within RSV bronchiolitis, little is known about its biologically-distinct endotypes. Here, we integrated clinical, virus, airway microbiome (species-level), transcriptome, and metabolome data of 221 infants hospitalized with RSV bronchiolitis in a multicentre prospective cohort study. We identified four biologically- and clinically-meaningful endotypes: A) clinicalclassicmicrobiomeM. nonliquefaciensinflammationIFN-intermediate, B) clinicalatopicmicrobiomeS. pneumoniae/M. catarrhalisinflammationIFN-high, C) clinicalseveremicrobiomemixedinflammationIFN-low, and D) clinicalnon-atopicmicrobiomeM.catarrhalisinflammationIL-6. Particularly, compared with endotype A infants, endotype B infants-who are characterized by a high proportion of IgE sensitization and rhinovirus coinfection, S. pneumoniae/M. catarrhalis codominance, and high IFN-α and -γ response-had a significantly higher risk for developing asthma (9% vs. 38%; OR, 6.00: 95%CI, 2.08-21.9; P = 0.002). Our findings provide an evidence base for the early identification of high-risk children during a critical period of airway development.
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Affiliation(s)
- Yoshihiko Raita
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Marcos Pérez-Losada
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, The George Washington University, Washington, DC, USA
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Robert J Freishtat
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA
- Division of Emergency Medicine, Children's National Hospital, Washington, DC, USA
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Brennan Harmon
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA
| | - Jonathan M Mansbach
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Pedro A Piedra
- Departments of Molecular Virology and Microbiology and Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Zhaozhong Zhu
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Carlos A Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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36
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Nicholson EG, Avadhanula V, Fragoso S, Stroh R, Ye X, Bond N, Santarcangelo P, Stroh J, Piedra PA. SARS-CoV-2 re-infection versus prolonged shedding: A case series. Influenza Other Respir Viruses 2021; 15:691-696. [PMID: 34085762 PMCID: PMC8242882 DOI: 10.1111/irv.12879] [Citation(s) in RCA: 3] [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: 04/30/2021] [Accepted: 05/16/2021] [Indexed: 01/15/2023] Open
Abstract
Since the start of the SARS‐CoV‐2 pandemic, it has been difficult to differentiate between SARS‐CoV‐2 re‐infection and prolonged RNA shedding. In this report, we identified patients with positive RT‐PCR results for SARS‐CoV‐2 ≥70 days apart. Clinical and laboratory data were collected and criteria were applied to discern whether the presentation was consistent with SARS‐CoV‐2 re‐infection or prolonged viral RNA shedding. Eleven individuals met the initial testing criteria, of which, seven met at least one criteria for re‐infection and four were consistent with prolonged RNA shedding. These data demonstrate the need for criteria to differentiate SARS‐CoV‐2 re‐infection from prolonged RNA shedding.
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Affiliation(s)
- Erin G Nicholson
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Sonia Fragoso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Rachel Stroh
- School of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Xunyan Ye
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Nanette Bond
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Patricia Santarcangelo
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - John Stroh
- Department of Emergency Medicine, St. Luke's Health, Houston, TX, USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
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37
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LaTurner ZW, Zong DM, Kalvapalle P, Gamas KR, Terwilliger A, Crosby T, Ali P, Avadhanula V, Santos HH, Weesner K, Hopkins L, Piedra PA, Maresso AW, Stadler LB. Evaluating recovery, cost, and throughput of different concentration methods for SARS-CoV-2 wastewater-based epidemiology. Water Res 2021; 197:117043. [PMID: 33784608 PMCID: PMC7957301 DOI: 10.1016/j.watres.2021.117043] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/12/2021] [Accepted: 03/10/2021] [Indexed: 05/18/2023]
Abstract
As the COVID-19 pandemic continues to affect communities across the globe, the need to contain the spread of the outbreaks is of paramount importance. Wastewater monitoring of the SARS-CoV-2 virus, the causative agent responsible for COVID-19, has emerged as a promising tool for health officials to anticipate outbreaks. As interest in wastewater monitoring continues to grow and municipalities begin to implement this approach, there is a need to further identify and evaluate methods used to concentrate SARS-CoV-2 virus RNA from wastewater samples. Here we evaluate the recovery, cost, and throughput of five different concentration methods for quantifying SARS-CoV-2 virus RNA in wastewater samples. We tested the five methods on six different wastewater samples. We also evaluated the use of a bovine coronavirus vaccine as a process control and pepper mild mottle virus as a normalization factor. Of the five methods we tested head-to-head, we found that HA filtration with bead beating performed the best in terms of sensitivity and cost. This evaluation can serve as a guide for laboratories establishing a protocol to perform wastewater monitoring of SARS-CoV-2.
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Affiliation(s)
- Zachary W LaTurner
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street MS 519, Houston, TX 77005, USA
| | - David M Zong
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street MS 519, Houston, TX 77005, USA
| | - Prashant Kalvapalle
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, 6100 Main Street MS 519, Houston, TX 77005, USA
| | - Kiara Reyes Gamas
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, 6100 Main Street MS 519, Houston, TX 77005, USA
| | - Austen Terwilliger
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Tessa Crosby
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street MS 519, Houston, TX 77005, USA
| | - Priyanka Ali
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street MS 519, Houston, TX 77005, USA
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Haroldo Hernandez Santos
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Kyle Weesner
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Loren Hopkins
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX 77054
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Anthony W Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Lauren B Stadler
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street MS 519, Houston, TX 77005, USA.
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Avadhanula V, Nicholson EG, Ferlic-Stark L, Piedra FA, Blunck BN, Fragoso S, Bond NL, Santarcangelo PL, Ye X, McBride TJ, Aideyan LO, Patel KD, Maurer L, Angelo LS, Piedra PA. Viral Load of Severe Acute Respiratory Syndrome Coronavirus 2 in Adults During the First and Second Wave of Coronavirus Disease 2019 Pandemic in Houston, Texas: The Potential of the Superspreader. J Infect Dis 2021; 223:1528-1537. [PMID: 33585934 PMCID: PMC7928726 DOI: 10.1093/infdis/jiab097] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/12/2021] [Indexed: 01/08/2023] Open
Abstract
Background During the COVID-19 pandemic, a minority of index cases are associated with a majority of secondary cases suggesting that super-spreaders could drive the pandemic. We identified a phenotype in individuals with extremely high viral load who could act as super-spreaders. Methods Data were analyzed from individuals tested for SARS-CoV-2 from March 18 through August 15, 2020. Outcomes were compared using contingency table and quantile regression to test the equality of medians between the pandemic waves and by viral load groups. Results Of the 11,564 samples tested, 1,319 (11.4%) were positive for SARS-CoV-2. An increase in weekly median viral load occurred in the second wave of the SARS-CoV2 pandemic. This population was more likely to be women, outpatients, symptomatic and have an extremely high or high viral load. In patients with multiple RT-PCR positive tests, the duration of viral shedding was comparable between individuals with asymptomatic/mild and mild/moderate illness severity. Conclusions We detected a small group of individuals with extremely high SARS-CoV-2 viral load with mild illness. We believe that these individuals’ characteristics could be consistent with the super-spreader phenomenon and that greater awareness of the social dynamics of these individuals is needed to understand the spread of SARS-CoV-2.
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Affiliation(s)
| | - Erin G Nicholson
- Department of Molecular Virology and Microbiology, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | | | | | - Brittani N Blunck
- Department of Molecular Virology and Microbiology, Houston, Texas, USA
| | - Sonia Fragoso
- Department of Molecular Virology and Microbiology, Houston, Texas, USA
| | - Nanette L Bond
- Department of Molecular Virology and Microbiology, Houston, Texas, USA
| | | | - Xunyan Ye
- Department of Molecular Virology and Microbiology, Houston, Texas, USA
| | - Trevor J McBride
- Department of Molecular Virology and Microbiology, Houston, Texas, USA
| | - Letisha O Aideyan
- Department of Molecular Virology and Microbiology, Houston, Texas, USA
| | - Kirtida D Patel
- Department of Molecular Virology and Microbiology, Houston, Texas, USA
| | - Lauren Maurer
- Department of Molecular Virology and Microbiology, Houston, Texas, USA
| | - Laura S Angelo
- Department of Molecular Virology and Microbiology, Houston, Texas, USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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39
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Ye X, Iwuchukwu OP, Avadhanula V, Aideyan LO, McBride TJ, Henke DM, Patel KD, Piedra FA, Angelo LS, Shah DP, Chemaly RF, Piedra PA. Humoral and Mucosal Antibody Response to RSV Structural Proteins in RSV-Infected Adult Hematopoietic Cell Transplant (HCT) Recipients. Viruses 2021; 13:v13060991. [PMID: 34073490 PMCID: PMC8228396 DOI: 10.3390/v13060991] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 05/06/2021] [Accepted: 05/24/2021] [Indexed: 11/16/2022] Open
Abstract
Respiratory syncytial virus (RSV) is an important cause of lower respiratory tract infection in infants, the elderly, and immunocompromised patients. RSV antibodies play a role in preventing reinfection and in clearance of RSV, but data regarding the levels of viral protein-specific antibodies elicited and their contribution to patient recovery from RSV-induced disease are limited. We prospectively enrolled a cohort of RSV-infected adult hematopoietic cell transplant (HCT) recipients (n = 40). Serum and nasal-wash samples were obtained at enrollment (acute samples) and convalescence (convalescent samples). We measured (1) humoral IgG and mucosal IgA binding antibody levels to multiple RSV proteins (F, G, N, P, and M2-1) by Western blot (WB); (2) neutralizing antibody (Nt Ab) titers by microneutralization assay; and (3) palivizumab-like antibody (PLA) concentrations by an ELISA-based competitive binding assay developed in the lab. Finally, we tested for correlations between protein-specific antibody levels and duration of viral shedding (normal: cleared in <14 days and delayed: cleared ≥14 days), as well as RSV/A and RSV/B subtypes. Convalescent sera from HCT recipients had significantly higher levels of anti-RSV antibodies to all 5 RSV structural proteins assayed (G, F, N, P, M2-1), higher Nt Abs to both RSV subtypes, and higher serum PLAs than at enrollment. Significantly higher levels of mucosal antibodies to 3 RSV structural proteins (G, N, and M2-1) were observed in the convalescent nasal wash versus acute nasal wash. Normal viral clearance group had significantly higher levels of serum IgG antibodies to F, N, and P viral proteins, higher Nt Ab to both RSV subtypes, and higher PLA, as well as higher levels of mucosal IgA antibodies to G and M2-1 viral proteins, and higher Nt Ab to both RSV subtypes compared to delayed viral clearance group. Normal RSV clearance was associated with higher IgG serum antibody levels to F and P viral proteins, and PLAs in convalescent serum (p < 0.05). Finally, overall antibody levels in RSV/A- and/B-infected HCT recipients were not significantly different. In summary, specific humoral and mucosal RSV antibodies are associated with viral clearance in HCT recipients naturally infected with RSV. In contrast to the humoral response, the F surface glycoprotein was not a major target of mucosal immunity. Our findings have implications for antigen selection in the development of RSV vaccines.
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Affiliation(s)
- Xunyan Ye
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (X.Y.); (O.P.I.); (V.A.); (L.O.A.); (T.J.M.); (D.M.H.); (K.D.P.); (F.-A.P.); (L.S.A.)
| | - Obinna P. Iwuchukwu
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (X.Y.); (O.P.I.); (V.A.); (L.O.A.); (T.J.M.); (D.M.H.); (K.D.P.); (F.-A.P.); (L.S.A.)
| | - Vasanthi Avadhanula
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (X.Y.); (O.P.I.); (V.A.); (L.O.A.); (T.J.M.); (D.M.H.); (K.D.P.); (F.-A.P.); (L.S.A.)
| | - Letisha O. Aideyan
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (X.Y.); (O.P.I.); (V.A.); (L.O.A.); (T.J.M.); (D.M.H.); (K.D.P.); (F.-A.P.); (L.S.A.)
| | - Trevor J. McBride
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (X.Y.); (O.P.I.); (V.A.); (L.O.A.); (T.J.M.); (D.M.H.); (K.D.P.); (F.-A.P.); (L.S.A.)
| | - David M. Henke
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (X.Y.); (O.P.I.); (V.A.); (L.O.A.); (T.J.M.); (D.M.H.); (K.D.P.); (F.-A.P.); (L.S.A.)
| | - Kirtida D. Patel
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (X.Y.); (O.P.I.); (V.A.); (L.O.A.); (T.J.M.); (D.M.H.); (K.D.P.); (F.-A.P.); (L.S.A.)
| | - Felipe-Andres Piedra
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (X.Y.); (O.P.I.); (V.A.); (L.O.A.); (T.J.M.); (D.M.H.); (K.D.P.); (F.-A.P.); (L.S.A.)
| | - Laura S. Angelo
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (X.Y.); (O.P.I.); (V.A.); (L.O.A.); (T.J.M.); (D.M.H.); (K.D.P.); (F.-A.P.); (L.S.A.)
| | - Dimpy P. Shah
- Department of Epidemiology and Biostatistics, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA;
| | - Roy F. Chemaly
- Departments of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Pedro A. Piedra
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (X.Y.); (O.P.I.); (V.A.); (L.O.A.); (T.J.M.); (D.M.H.); (K.D.P.); (F.-A.P.); (L.S.A.)
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Correspondence:
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40
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Dawood FS, Varner M, Munoz F, Stockwell MS, Suyama J, Li DK, Tita A, Mathias L, Shakib JH, Piedra PA, Gyamfi-Bannerman C, Weissman A, Ferber J, Battarbee AN, Wesley MG, Vorwaller K, Powers E, Gibson M, Bond N, Santarcangelo P, Avadhanula V, Newes-Adeyi G, Hunt DR, Subramaniam A, Sanusi A, Boone A, Ogokeh C, Macio I, Odouli R, Thind P, Vargas CY, Almonte C, Galang R, Shapiro-Mendoza C, Campbell AP. Respiratory Viral Infections and Infection Prevention Practices among Women with Acute Respiratory Illness during Delivery Hospitalizations during the 2019-2020 Influenza Season. J Infect Dis 2021; 225:50-54. [PMID: 34037764 DOI: 10.1093/infdis/jiab292] [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: 04/10/2021] [Accepted: 05/21/2021] [Indexed: 11/12/2022] Open
Abstract
We conducted a cross-sectional study of pregnant women with acute respiratory illness during delivery hospitalizations in influenza season to describe clinical testing for respiratory viruses and infection prevention practices. Women had nasal swabs tested for influenza and other respiratory viruses. Among 91 enrolled women, 22 (24%) had clinical testing for influenza. Based on clinical and study testing combined, 41/91 (45%) women had samples positive for respiratory viruses. The most common virus was influenza (17/91, 19%); 53% (9/17) of influenza virus infections were identified through study testing alone. Only 16% of women were on droplet precautions. Peripartum respiratory infections may be underrecognized.
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Affiliation(s)
- Fatimah S Dawood
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Michael Varner
- Department of Obstetrics and Gynecology, University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | - Flor Munoz
- Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Melissa S Stockwell
- Division of Child and Adolescent Health, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.,Department of Population and Family Health, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY, USA.,New York-Presbyterian Hospital, New York, NY, USA
| | - Joe Suyama
- Department of Emergency Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - De-Kun Li
- Division of Research, Kaiser Foundation Research Institute, Kaiser Permanente, Oakland, CA, USA
| | - Alan Tita
- Center for Women's Reproductive Health and Department of Obstetrics and Gynecology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Julie H Shakib
- Department of Obstetrics and Gynecology, University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | - Pedro A Piedra
- Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Cynthia Gyamfi-Bannerman
- New York-Presbyterian Hospital, New York, NY, USA.,Department of OBGYN, Division of Maternal-Fetal Medicine, Columbia University Irving Medical Center, USA
| | - Alexandra Weissman
- Department of Emergency Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jeannette Ferber
- Division of Research, Kaiser Foundation Research Institute, Kaiser Permanente, Oakland, CA, USA
| | - Ashley N Battarbee
- Center for Women's Reproductive Health and Department of Obstetrics and Gynecology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Kelly Vorwaller
- Department of Obstetrics and Gynecology, University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | - Emily Powers
- Department of Obstetrics and Gynecology, University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | - Marie Gibson
- Department of Obstetrics and Gynecology, University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | - Nanette Bond
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Patricia Santarcangelo
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | | | | | - Akila Subramaniam
- Center for Women's Reproductive Health and Department of Obstetrics and Gynecology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ayodeji Sanusi
- Center for Women's Reproductive Health and Department of Obstetrics and Gynecology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Amy Boone
- Center for Women's Reproductive Health and Department of Obstetrics and Gynecology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Constance Ogokeh
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ingrid Macio
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh Medical Center Magee-Womens Hospital, Pittsburgh, PA, USA
| | - Roxana Odouli
- Division of Research, Kaiser Foundation Research Institute, Kaiser Permanente, Oakland, CA, USA
| | - Priyam Thind
- Division of Child and Adolescent Health, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Celibell Y Vargas
- Division of Child and Adolescent Health, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Casandra Almonte
- Department of OBGYN, Division of Maternal-Fetal Medicine, Columbia University Irving Medical Center, USA
| | - Romeo Galang
- Division of Reproductive Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Carrie Shapiro-Mendoza
- Division of Reproductive Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Angela P Campbell
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Abstract
INTRODUCTION Respiratory Syncytial Virus (RSV) is a leading cause of acute lower respiratory infections worldwide. The RSV fusion (F) glycoprotein is a major focus of vaccine development. Despite over 60 years of research, there is no licensed vaccine for RSV. AREAS COVERED The primary focus of this review is a novel RSV-F recombinant nanoparticle vaccine from Novavax utilizing the F protein, a conserved and immunodominant surface glycoprotein. This RSV F recombinant nanoparticle vaccine adsorbed to 0.4 mg of aluminum phosphate was ultimately administered by a single intramuscular injection during the third trimester of pregnancy in an effort to induce passive immunity in newborns. Its mechanism, performance in clinical trials, and place in RSV vaccine history are discussed. EXPERT OPINION The vaccine was safe and well tolerated in pregnant women and the results suggest potential benefits with respect to other medically relevant end-point events involving RSV-associated respiratory and all-cause disease in infants. However, the RSV-F recombinant nanoparticle vaccine did not meet the pre-specified primary success criteria for efficacy against RSV-associated, medically significant lower respiratory tract infection in infants up to 90 days of life. The potential benefits to infants from maternal immunization and excellent safety profile warrant further confirmatory studies.
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Affiliation(s)
- Brittani N Blunck
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, USA
| | - Wanderson Rezende
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, USA.,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, United States
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42
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Symanski E, Ensor KB, Piedra PA, Sheth K, Caton K, Williams SL, Persse D, Banerjee D, Hopkins L. Population-Based Estimates of SARS-CoV-2 Seroprevalence in Houston, TX as of September 2020. J Infect Dis 2021; 224:1649-1657. [PMID: 33914068 PMCID: PMC8135754 DOI: 10.1093/infdis/jiab203] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 04/08/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND In contrast to studies that relied on volunteers or convenience sampling, there are few population-based SARS-CoV-2 seroprevalence investigations and most were conducted early in the pandemic. The health department of the fourth largest city in the U.S. recognized that sound estimates of viral impact were needed to inform decision-making. METHODS Adapting standardized disaster research methodology in September 2020, the city was divided into high and low strata based on RT-PCR positivity rates, and census block groups within each stratum were randomly selected with probability proportional to size, followed by random selection of households within each group. Using two immunoassays, the proportion of infected individuals was estimated for the city, as well as by positivity rate and by sociodemographic and other characteristics. The degree of under ascertainment of seroprevalence was estimated based on RT-PCR positive cases. RESULTS Seroprevalence was estimated to be 14% with a near two-fold difference in areas with high (18%) versus low (10%) RT-PCR positivity rates and was four times higher compared to case-based surveillance data. CONCLUSIONS Seroprevalence was higher than previously reported and is greater than that estimated from RT-PCR data. Results will be used to inform public health decisions about testing, outreach, and vaccine rollout.
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Affiliation(s)
- Elaine Symanski
- Center for Precision Environmental Health, Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, TX, USA
| | | | - Pedro A Piedra
- Departments of Molecular Virology and Microbiology, and Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | | | | | | | - David Persse
- Houston Health Department, Houston, TX, USA.,Departments of Emergency Medicine and Surgery, Baylor College of Medicine, Houston, TX, USA
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43
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Blunck BN, Aideyan L, Ye X, Avadhanula V, Ferlic-Stark L, Zechiedrich L, Gilbert BE, Piedra PA. A prospective surveillance study on the kinetics of the humoral immune response to the respiratory syncytial virus fusion protein in adults in Houston, Texas. Vaccine 2021; 39:1248-1256. [PMID: 33509697 DOI: 10.1016/j.vaccine.2021.01.045] [Citation(s) in RCA: 15] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/12/2020] [Accepted: 01/16/2021] [Indexed: 12/15/2022]
Abstract
Respiratory syncytial virus (RSV)-specific serum antibody has been correlated to protection of infection and reduction of severe disease, but reinfection is still frequent. In this study, we evaluated RSV-specific serum antibody activity following natural RSV re-infection to examine the longevity of the humoral immune response in adults. Nineteen healthy adult volunteers under sixty-five years of age were enrolled during the 2018-2019 RSV season in Houston, TX. Blood was collected at three study visits. The kinetics of RSV-neutralizing, RSV F site-specific competitive, and RSV-binding antibodies in serum samples were measured by microneutralization and enzyme-linked immunosorbent assays. Three distinct profiles of RSV-specific antibody kinetics were identified that were consistent with RSV infection status: uninfected, acutely infected, and recently infected. The uninfected group had stable antibody titers for the duration of the study period (185 days). The acutely infected group had lower antibody responses at the beginning of the study, supporting a correlate of infection, followed by a significant antibody response after infection that was maintained for at least 125 days. Unlike the acutely infected group, the recently infected group had a significant precipitous decrease in RSV antibody in only 60 days. This study is the first, to our knowledge, to describe this abrupt loss of RSV-specific antibody in detail. This rapid decline of antibody may present an obstacle for the development of vaccines with lasting protection against RSV, and perhaps other respiratory pathogens. Neutralizing antibody responses were greater to prototypic than contemporaneous RSV strains, regardless of infection status, indicating that original antigenic sin may impact the humoral immune response to new or emerging RSV strains.
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Affiliation(s)
| | - Letisha Aideyan
- Department of Molecular Virology and Microbiology, United States
| | - Xunyan Ye
- Department of Molecular Virology and Microbiology, United States
| | | | | | - Lynn Zechiedrich
- Department of Molecular Virology and Microbiology, United States; Verna and Marrs McLean, Department of Biochemistry and Molecular Biology, United States; Department of Pharmacology and Chemical Biology, United States
| | - Brian E Gilbert
- Department of Molecular Virology and Microbiology, United States
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, United States; Department of Pediatrics, Baylor College of Medicine, United States.
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Tian JH, Patel N, Haupt R, Zhou H, Weston S, Hammond H, Logue J, Portnoff AD, Norton J, Guebre-Xabier M, Zhou B, Jacobson K, Maciejewski S, Khatoon R, Wisniewska M, Moffitt W, Kluepfel-Stahl S, Ekechukwu B, Papin J, Boddapati S, Jason Wong C, Piedra PA, Frieman MB, Massare MJ, Fries L, Bengtsson KL, Stertman L, Ellingsworth L, Glenn G, Smith G. SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 immunogenicity in baboons and protection in mice. Nat Commun 2021; 12:372. [PMID: 33446655 PMCID: PMC7809486 DOI: 10.1038/s41467-020-20653-8] [Citation(s) in RCA: 296] [Impact Index Per Article: 98.7] [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: 06/30/2020] [Accepted: 12/08/2020] [Indexed: 02/08/2023] Open
Abstract
The COVID-19 pandemic continues to spread throughout the world with an urgent need for a safe and protective vaccine to effectuate herd protection and control the spread of SARS-CoV-2. Here, we report the development of a SARS-CoV-2 subunit vaccine (NVX-CoV2373) from the full-length spike (S) protein that is stable in the prefusion conformation. NVX-CoV2373 S form 27.2-nm nanoparticles that are thermostable and bind with high affinity to the human angiotensin-converting enzyme 2 (hACE2) receptor. In mice, low-dose NVX-CoV2373 with saponin-based Matrix-M adjuvant elicit high titer anti-S IgG that blocks hACE2 receptor binding, neutralize virus, and protects against SARS-CoV-2 challenge with no evidence of vaccine-associated enhanced respiratory disease. NVX-CoV2373 also elicits multifunctional CD4+ and CD8+ T cells, CD4+ follicular helper T cells (Tfh), and antigen-specific germinal center (GC) B cells in the spleen. In baboons, low-dose levels of NVX-CoV2373 with Matrix-M was also highly immunogenic and elicited high titer anti-S antibodies and functional antibodies that block S-protein binding to hACE2 and neutralize virus infection and antigen-specific T cells. These results support the ongoing phase 1/2 clinical evaluation of the safety and immunogenicity of NVX-CoV2373 with Matrix-M (NCT04368988).
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Affiliation(s)
- Jing-Hui Tian
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | - Nita Patel
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | - Robert Haupt
- University of Maryland, School of Medicine, 685 West Baltimore St, Baltimore, MD, 21201, USA
| | - Haixia Zhou
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | - Stuart Weston
- University of Maryland, School of Medicine, 685 West Baltimore St, Baltimore, MD, 21201, USA
| | - Holly Hammond
- University of Maryland, School of Medicine, 685 West Baltimore St, Baltimore, MD, 21201, USA
| | - James Logue
- University of Maryland, School of Medicine, 685 West Baltimore St, Baltimore, MD, 21201, USA
| | | | - James Norton
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | | | - Bin Zhou
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | - Kelsey Jacobson
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | | | - Rafia Khatoon
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | | | - Will Moffitt
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | | | - Betty Ekechukwu
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | - James Papin
- Department of Pathology, Division of Comparative Medicine, University of Oklahoma, Health Sciences Center, 940 Stanton L. Young, BMS 203, Oklahoma City, OK, 73104, USA
| | - Sarathi Boddapati
- Catalent Cell & Gene Therapy, 20 Firstfield Road, Gaithersburg, MD, 20874, USA
| | - C Jason Wong
- Catalent Cell & Gene Therapy, 20 Firstfield Road, Gaithersburg, MD, 20874, USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, and Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Matthew B Frieman
- University of Maryland, School of Medicine, 685 West Baltimore St, Baltimore, MD, 21201, USA
| | | | - Louis Fries
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | | | | | | | - Gregory Glenn
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | - Gale Smith
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD, 20878, USA.
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45
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Tian JH, Patel N, Haupt R, Zhou H, Weston S, Hammond H, Logue J, Portnoff AD, Norton J, Guebre-Xabier M, Zhou B, Jacobson K, Maciejewski S, Khatoon R, Wisniewska M, Moffitt W, Kluepfel-Stahl S, Ekechukwu B, Papin J, Boddapati S, Jason Wong C, Piedra PA, Frieman MB, Massare MJ, Fries L, Bengtsson KL, Stertman L, Ellingsworth L, Glenn G, Smith G. SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 immunogenicity in baboons and protection in mice. Nat Commun 2021; 12:372. [PMID: 33446655 DOI: 10.1101/2020.06.29.178509] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/08/2020] [Indexed: 05/28/2023] Open
Abstract
The COVID-19 pandemic continues to spread throughout the world with an urgent need for a safe and protective vaccine to effectuate herd protection and control the spread of SARS-CoV-2. Here, we report the development of a SARS-CoV-2 subunit vaccine (NVX-CoV2373) from the full-length spike (S) protein that is stable in the prefusion conformation. NVX-CoV2373 S form 27.2-nm nanoparticles that are thermostable and bind with high affinity to the human angiotensin-converting enzyme 2 (hACE2) receptor. In mice, low-dose NVX-CoV2373 with saponin-based Matrix-M adjuvant elicit high titer anti-S IgG that blocks hACE2 receptor binding, neutralize virus, and protects against SARS-CoV-2 challenge with no evidence of vaccine-associated enhanced respiratory disease. NVX-CoV2373 also elicits multifunctional CD4+ and CD8+ T cells, CD4+ follicular helper T cells (Tfh), and antigen-specific germinal center (GC) B cells in the spleen. In baboons, low-dose levels of NVX-CoV2373 with Matrix-M was also highly immunogenic and elicited high titer anti-S antibodies and functional antibodies that block S-protein binding to hACE2 and neutralize virus infection and antigen-specific T cells. These results support the ongoing phase 1/2 clinical evaluation of the safety and immunogenicity of NVX-CoV2373 with Matrix-M (NCT04368988).
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MESH Headings
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/immunology
- Animals
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- COVID-19/genetics
- COVID-19/immunology
- COVID-19/prevention & control
- COVID-19/virology
- COVID-19 Vaccines/administration & dosage
- COVID-19 Vaccines/genetics
- COVID-19 Vaccines/immunology
- Disease Models, Animal
- Female
- Male
- Mice
- Mice, Inbred BALB C
- Papio
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/administration & dosage
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- T-Lymphocytes/immunology
- Vaccines, Subunit/administration & dosage
- Vaccines, Subunit/genetics
- Vaccines, Subunit/immunology
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Affiliation(s)
- Jing-Hui Tian
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | - Nita Patel
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | - Robert Haupt
- University of Maryland, School of Medicine, 685 West Baltimore St, Baltimore, MD, 21201, USA
| | - Haixia Zhou
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | - Stuart Weston
- University of Maryland, School of Medicine, 685 West Baltimore St, Baltimore, MD, 21201, USA
| | - Holly Hammond
- University of Maryland, School of Medicine, 685 West Baltimore St, Baltimore, MD, 21201, USA
| | - James Logue
- University of Maryland, School of Medicine, 685 West Baltimore St, Baltimore, MD, 21201, USA
| | | | - James Norton
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | | | - Bin Zhou
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | - Kelsey Jacobson
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | | | - Rafia Khatoon
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | | | - Will Moffitt
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | | | - Betty Ekechukwu
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | - James Papin
- Department of Pathology, Division of Comparative Medicine, University of Oklahoma, Health Sciences Center, 940 Stanton L. Young, BMS 203, Oklahoma City, OK, 73104, USA
| | - Sarathi Boddapati
- Catalent Cell & Gene Therapy, 20 Firstfield Road, Gaithersburg, MD, 20874, USA
| | - C Jason Wong
- Catalent Cell & Gene Therapy, 20 Firstfield Road, Gaithersburg, MD, 20874, USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, and Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Matthew B Frieman
- University of Maryland, School of Medicine, 685 West Baltimore St, Baltimore, MD, 21201, USA
| | | | - Louis Fries
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | | | | | | | - Gregory Glenn
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | - Gale Smith
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD, 20878, USA.
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Doddapaneni H, Cregeen SJ, Sucgang R, Meng Q, Qin X, Avadhanula V, Chao H, Menon V, Nicholson E, Henke D, Piedra FA, Rajan A, Momin Z, Kottapalli K, Hoffman KL, Sedlazeck FJ, Metcalf G, Piedra PA, Muzny DM, Petrosino JF, Gibbs RA. Oligonucleotide Capture Sequencing of the SARS-CoV-2 Genome and Subgenomic Fragments from COVID-19 Individuals. bioRxiv 2020:2020.12.11.421057. [PMID: 33330863 PMCID: PMC7743067 DOI: 10.1101/2020.12.11.421057] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 01/10/2023]
Abstract
The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity and provided evidence of expression of ORF10. Heterogeneous allelic frequencies along the 20kb ORF1ab gene suggested the presence of a defective interfering viral RNA species subpopulation in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.
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Affiliation(s)
- Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sara Javornik Cregeen
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard Sucgang
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Houston, Texas, United States of America, USA
| | - Hsu Chao
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Vipin Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Erin Nicholson
- Department of Molecular Virology and Microbiology, Houston, Texas, United States of America, USA
- Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America, USA
| | - David Henke
- Department of Molecular Virology and Microbiology, Houston, Texas, United States of America, USA
| | - Felipe-Andres Piedra
- Department of Molecular Virology and Microbiology, Houston, Texas, United States of America, USA
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Houston, Texas, United States of America, USA
| | - Zeineen Momin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kavya Kottapalli
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kristi L. Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Houston, Texas, United States of America, USA
- Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America, USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph F. Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
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47
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Keech C, Albert G, Cho I, Robertson A, Reed P, Neal S, Plested JS, Zhu M, Cloney-Clark S, Zhou H, Smith G, Patel N, Frieman MB, Haupt RE, Logue J, McGrath M, Weston S, Piedra PA, Desai C, Callahan K, Lewis M, Price-Abbott P, Formica N, Shinde V, Fries L, Lickliter JD, Griffin P, Wilkinson B, Glenn GM. Phase 1-2 Trial of a SARS-CoV-2 Recombinant Spike Protein Nanoparticle Vaccine. N Engl J Med 2020; 383:2320-2332. [PMID: 32877576 PMCID: PMC7494251 DOI: 10.1056/nejmoa2026920] [Citation(s) in RCA: 819] [Impact Index Per Article: 204.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND NVX-CoV2373 is a recombinant severe acute respiratory syndrome coronavirus 2 (rSARS-CoV-2) nanoparticle vaccine composed of trimeric full-length SARS-CoV-2 spike glycoproteins and Matrix-M1 adjuvant. METHODS We initiated a randomized, placebo-controlled, phase 1-2 trial to evaluate the safety and immunogenicity of the rSARS-CoV-2 vaccine (in 5-μg and 25-μg doses, with or without Matrix-M1 adjuvant, and with observers unaware of trial-group assignments) in 131 healthy adults. In phase 1, vaccination comprised two intramuscular injections, 21 days apart. The primary outcomes were reactogenicity; laboratory values (serum chemistry and hematology), according to Food and Drug Administration toxicity scoring, to assess safety; and IgG anti-spike protein response (in enzyme-linked immunosorbent assay [ELISA] units). Secondary outcomes included unsolicited adverse events, wild-type virus neutralization (microneutralization assay), and T-cell responses (cytokine staining). IgG and microneutralization assay results were compared with 32 (IgG) and 29 (neutralization) convalescent serum samples from patients with Covid-19, most of whom were symptomatic. We performed a primary analysis at day 35. RESULTS After randomization, 83 participants were assigned to receive the vaccine with adjuvant and 25 without adjuvant, and 23 participants were assigned to receive placebo. No serious adverse events were noted. Reactogenicity was absent or mild in the majority of participants, more common with adjuvant, and of short duration (mean, ≤2 days). One participant had mild fever that lasted 1 day. Unsolicited adverse events were mild in most participants; there were no severe adverse events. The addition of adjuvant resulted in enhanced immune responses, was antigen dose-sparing, and induced a T helper 1 (Th1) response. The two-dose 5-μg adjuvanted regimen induced geometric mean anti-spike IgG (63,160 ELISA units) and neutralization (3906) responses that exceeded geometric mean responses in convalescent serum from mostly symptomatic Covid-19 patients (8344 and 983, respectively). CONCLUSIONS At 35 days, NVX-CoV2373 appeared to be safe, and it elicited immune responses that exceeded levels in Covid-19 convalescent serum. The Matrix-M1 adjuvant induced CD4+ T-cell responses that were biased toward a Th1 phenotype. (Funded by the Coalition for Epidemic Preparedness Innovations; ClinicalTrials.gov number, NCT04368988).
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Affiliation(s)
- Cheryl Keech
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Gary Albert
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Iksung Cho
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Andreana Robertson
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Patricia Reed
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Susan Neal
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Joyce S Plested
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Mingzhu Zhu
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Shane Cloney-Clark
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Haixia Zhou
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Gale Smith
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Nita Patel
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Matthew B Frieman
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Robert E Haupt
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - James Logue
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Marisa McGrath
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Stuart Weston
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Pedro A Piedra
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Chinar Desai
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Kathleen Callahan
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Maggie Lewis
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Patricia Price-Abbott
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Neil Formica
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Vivek Shinde
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Louis Fries
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Jason D Lickliter
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Paul Griffin
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Bethanie Wilkinson
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Gregory M Glenn
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
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Keech C, Albert G, Cho I, Robertson A, Reed P, Neal S, Plested JS, Zhu M, Cloney-Clark S, Zhou H, Smith G, Patel N, Frieman MB, Haupt RE, Logue J, McGrath M, Weston S, Piedra PA, Desai C, Callahan K, Lewis M, Price-Abbott P, Formica N, Shinde V, Fries L, Lickliter JD, Griffin P, Wilkinson B, Glenn GM. Phase 1-2 Trial of a SARS-CoV-2 Recombinant Spike Protein Nanoparticle Vaccine. N Engl J Med 2020. [PMID: 32877576 DOI: 10.1056/nejmoa2026920.)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
BACKGROUND NVX-CoV2373 is a recombinant severe acute respiratory syndrome coronavirus 2 (rSARS-CoV-2) nanoparticle vaccine composed of trimeric full-length SARS-CoV-2 spike glycoproteins and Matrix-M1 adjuvant. METHODS We initiated a randomized, placebo-controlled, phase 1-2 trial to evaluate the safety and immunogenicity of the rSARS-CoV-2 vaccine (in 5-μg and 25-μg doses, with or without Matrix-M1 adjuvant, and with observers unaware of trial-group assignments) in 131 healthy adults. In phase 1, vaccination comprised two intramuscular injections, 21 days apart. The primary outcomes were reactogenicity; laboratory values (serum chemistry and hematology), according to Food and Drug Administration toxicity scoring, to assess safety; and IgG anti-spike protein response (in enzyme-linked immunosorbent assay [ELISA] units). Secondary outcomes included unsolicited adverse events, wild-type virus neutralization (microneutralization assay), and T-cell responses (cytokine staining). IgG and microneutralization assay results were compared with 32 (IgG) and 29 (neutralization) convalescent serum samples from patients with Covid-19, most of whom were symptomatic. We performed a primary analysis at day 35. RESULTS After randomization, 83 participants were assigned to receive the vaccine with adjuvant and 25 without adjuvant, and 23 participants were assigned to receive placebo. No serious adverse events were noted. Reactogenicity was absent or mild in the majority of participants, more common with adjuvant, and of short duration (mean, ≤2 days). One participant had mild fever that lasted 1 day. Unsolicited adverse events were mild in most participants; there were no severe adverse events. The addition of adjuvant resulted in enhanced immune responses, was antigen dose-sparing, and induced a T helper 1 (Th1) response. The two-dose 5-μg adjuvanted regimen induced geometric mean anti-spike IgG (63,160 ELISA units) and neutralization (3906) responses that exceeded geometric mean responses in convalescent serum from mostly symptomatic Covid-19 patients (8344 and 983, respectively). CONCLUSIONS At 35 days, NVX-CoV2373 appeared to be safe, and it elicited immune responses that exceeded levels in Covid-19 convalescent serum. The Matrix-M1 adjuvant induced CD4+ T-cell responses that were biased toward a Th1 phenotype. (Funded by the Coalition for Epidemic Preparedness Innovations; ClinicalTrials.gov number, NCT04368988).
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Affiliation(s)
- Cheryl Keech
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Gary Albert
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Iksung Cho
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Andreana Robertson
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Patricia Reed
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Susan Neal
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Joyce S Plested
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Mingzhu Zhu
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Shane Cloney-Clark
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Haixia Zhou
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Gale Smith
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Nita Patel
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Matthew B Frieman
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Robert E Haupt
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - James Logue
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Marisa McGrath
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Stuart Weston
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Pedro A Piedra
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Chinar Desai
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Kathleen Callahan
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Maggie Lewis
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Patricia Price-Abbott
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Neil Formica
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Vivek Shinde
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Louis Fries
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Jason D Lickliter
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Paul Griffin
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Bethanie Wilkinson
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
| | - Gregory M Glenn
- From Novavax, Gaithersburg, MD (C.K., G.A., I.C., A.R., P.R., S.N., J.S.P., M.Z., S.C.-C., H.Z., G.S., N.P., C.D., K.C., M.L., P.P.-A., N.F., V.S., L.F., B.W., G.M.G.), and the University of Maryland School of Medicine, Baltimore (M.B.F., R.E.H., J.L., M.M.G., S.W.); Baylor College of Medicine, Houston (P.A.P.); and Nucleus Network, Melbourne, VIC (J.D.L.), and Q-Pharm, Herston, QLD (P.G.) - both in Australia
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49
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Guebre-Xabier M, Patel N, Tian JH, Zhou B, Maciejewski S, Lam K, Portnoff AD, Massare MJ, Frieman MB, Piedra PA, Ellingsworth L, Glenn G, Smith G. NVX-CoV2373 vaccine protects cynomolgus macaque upper and lower airways against SARS-CoV-2 challenge. Vaccine 2020; 38:7892-7896. [PMID: 33139139 DOI: 10.1101/2020.08.18.256578] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/02/2020] [Accepted: 10/19/2020] [Indexed: 05/28/2023]
Abstract
There is an urgent need for a safe and protective vaccine to control the global spread of SARS-CoV-2 and prevent COVID-19. Here, we report the immunogenicity and protective efficacy of a SARS-CoV-2 subunit vaccine (NVX-CoV2373) produced from the full-length SARS-CoV-2 spike (S) glycoprotein stabilized in the prefusion conformation. Cynomolgus macaques (Macaca fascicularis) immunized with NVX-CoV2373 and the saponin-based Matrix-M™ adjuvant induced anti-S antibody that was neutralizing and blocked binding to the human angiotensin-converting enzyme 2 (hACE2) receptor. Following intranasal and intratracheal challenge with SARS-CoV-2, immunized macaques were protected against upper and lower infection and pulmonary disease. These results support ongoing phase 1/2 clinical studies of the safety and immunogenicity of NVX-CoV2327 vaccine (NCT04368988).
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Affiliation(s)
| | - Nita Patel
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA.
| | - Jing-Hui Tian
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA.
| | - Bin Zhou
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA.
| | | | - Kristal Lam
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA.
| | | | | | - Matthew B Frieman
- University of Maryland, School of Medicine, 685 West Baltimore St, Baltimore, MD 21201, USA.
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, and Pediatrics, Baylor College of Medicine, Houston, TX, USA.
| | | | - Gregory Glenn
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA.
| | - Gale Smith
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA.
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50
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Guebre-Xabier M, Patel N, Tian JH, Zhou B, Maciejewski S, Lam K, Portnoff AD, Massare MJ, Frieman MB, Piedra PA, Ellingsworth L, Glenn G, Smith G. NVX-CoV2373 vaccine protects cynomolgus macaque upper and lower airways against SARS-CoV-2 challenge. Vaccine 2020; 38:7892-7896. [PMID: 33139139 PMCID: PMC7584426 DOI: 10.1016/j.vaccine.2020.10.064] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [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: 08/19/2020] [Revised: 10/02/2020] [Accepted: 10/19/2020] [Indexed: 11/21/2022]
Abstract
There is an urgent need for a safe and protective vaccine to control the global spread of SARS-CoV-2 and prevent COVID-19. Here, we report the immunogenicity and protective efficacy of a SARS-CoV-2 subunit vaccine (NVX-CoV2373) produced from the full-length SARS-CoV-2 spike (S) glycoprotein stabilized in the prefusion conformation. Cynomolgus macaques (Macaca fascicularis) immunized with NVX-CoV2373 and the saponin-based Matrix-M™ adjuvant induced anti-S antibody that was neutralizing and blocked binding to the human angiotensin-converting enzyme 2 (hACE2) receptor. Following intranasal and intratracheal challenge with SARS-CoV-2, immunized macaques were protected against upper and lower infection and pulmonary disease. These results support ongoing phase 1/2 clinical studies of the safety and immunogenicity of NVX-CoV2327 vaccine (NCT04368988).
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Affiliation(s)
| | - Nita Patel
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA.
| | - Jing-Hui Tian
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA.
| | - Bin Zhou
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA.
| | | | - Kristal Lam
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA.
| | | | | | - Matthew B Frieman
- University of Maryland, School of Medicine, 685 West Baltimore St, Baltimore, MD 21201, USA.
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, and Pediatrics, Baylor College of Medicine, Houston, TX, USA.
| | | | - Gregory Glenn
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA.
| | - Gale Smith
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA.
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