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Janoff EN, Shih MC, Donskey C, Belitskaya-Levy I, Brau N, Rodriguez-Barradas MC, Chan E, Zimmerman P, Miller EK, Vaughan LB, Daniel Markley J, Goldberg AM, Sriram P, Anzueto A, Uyeda L, Zehm L, Wills A, Hutchinson C, Jones L, Peterson D, Ringer RJ, Dumont L, Gleason T, Bonomo RA, Curtis JL, Brown ST. Impact of High-Titer Convalescent Plasma on Clinical and Virologic Outcomes Among Veterans Hospitalized With SARS-CoV-2 Infection: VA CoronavirUs Research and Efficacy Studies-1 (VA CURES-1). J Med Virol 2025; 97:e70349. [PMID: 40400480 DOI: 10.1002/jmv.70349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Revised: 01/26/2025] [Accepted: 03/27/2025] [Indexed: 05/23/2025]
Abstract
In the initial absence of proven therapies, empirical COVID-19 convalescent plasma (CCP) was rapidly introduced for individuals hospitalized for COVID-19. Seventy-five participants were randomized from November 2020 to June 2021 in a double-blind, multi-site, placebo-controlled, randomized trial (VA CURES-1) evaluating the impact of CCP vs. saline in Veterans hospitalized with COVID-19 with hypoxemia. The composite primary outcome was acute hypoxemic respiratory failure or all-cause death by Day 29. We analyzed clinical outcomes, nasal viral RNA, plasma cytokines and viral evolution over time. Among 40 participants receiving saline and 35 receiving CCP with high neutralizing titers (median 1:1420), the percent reaching the primary outcome was similar (10%), as were time to clinical recovery and to nasal viral clearance. By whole genome sequencing, viral molecular complexity evolved pre- to posttreatment more frequently in recipients of saline vs. CCP (4 of 7 (57.1%) vs. 1 of 4 (25%), respectively), based on numbers of mixed allele positions. Numbers of amino acid-changing, non-synonymous mutations in the spike protein were greater in saline vs. CCP recipients. Both outcomes suggested purifying selection (reduced overall viral infection complexity) following CCP. In conclusion, convalescent plasma showed no significant clinical impact but may influence SARS-CoV-2 complexity. Trial Registration: ClinicalTrials.gov Identifier: NCT04539275.
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Affiliation(s)
- Edward N Janoff
- Rocky Mountain Regional VA Medical Center, Aurora, Colorado, USA
- University of Colorado Denver School of Medicine, Aurora, Colorado, USA
| | - Mei-Chiung Shih
- Department of Veterans Affairs, Cooperative Studies Program Coordinating Center, Palo Alto, California, USA
- Stanford University School of Medicine, Stanford, California, USA
| | - Curtis Donskey
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Louis Stokes Cleveland VA Medical Center, Cleveland, Ohio, USA
| | - Ilana Belitskaya-Levy
- Department of Veterans Affairs, Cooperative Studies Program Coordinating Center, Palo Alto, California, USA
| | - Norbert Brau
- James J. Peters Department of Veterans Affairs Medical Center, Bronx, New York, USA
- Icahn School of Medicine at Mt. Sinai, New York, New York, USA
| | | | - Ernest Chan
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Peter Zimmerman
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Elliott K Miller
- Department of Veterans Affairs, Cooperative Studies Program Clinical Research Pharmacy Coordinating Center, Albuquerque, New Mexico, USA
| | - Leroy B Vaughan
- Central Virginia VA Healthcare System, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - J Daniel Markley
- Central Virginia VA Healthcare System, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Alexa M Goldberg
- Department of Veterans Affairs, Cooperative Studies Program Clinical Research Pharmacy Coordinating Center, Albuquerque, New Mexico, USA
| | - Peruvemba Sriram
- North Florida/South Georgia Veteran's Health System, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Antonio Anzueto
- South Texas Veterans Healthcare System, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Lauren Uyeda
- Department of Veterans Affairs, Cooperative Studies Program Coordinating Center, Palo Alto, California, USA
| | - Lisa Zehm
- Department of Veterans Affairs, Cooperative Studies Program Coordinating Center, Palo Alto, California, USA
| | - Ashlea Wills
- Rocky Mountain Regional VA Medical Center, Aurora, Colorado, USA
| | | | - Lucas Jones
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Louis Stokes Cleveland VA Medical Center, Cleveland, Ohio, USA
| | - Dianne Peterson
- VA CSP Albuquerque Central Biorepository, Albuquerque, New Mexico, USA
| | - Robert J Ringer
- VA CSP Albuquerque Central Biorepository, Albuquerque, New Mexico, USA
| | - Larry Dumont
- Vitalant Research Institute, Aurora, Colorado, USA
| | - Theresa Gleason
- Department of Veterans Affairs, Cooperative Studies Program Clinical Science ResearcPharmacy Coordinating Center, Washington, DC, USA
| | - Robert A Bonomo
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Louis Stokes Cleveland VA Medical Center, Cleveland, Ohio, USA
| | - Jeffrey L Curtis
- VA Ann Arbor Healthcare System, Ann Arbor, Michigan, USA
- University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Sheldon T Brown
- James J. Peters Department of Veterans Affairs Medical Center, Bronx, New York, USA
- Icahn School of Medicine at Mt. Sinai, New York, New York, USA
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2
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Tai JH, Lee DC, Lin HF, Chao TL, Ruan Y, Cheng YW, Chou YC, Lin YY, Chang SY, Chen PJ, Yeh SH, Wang HY. Tradeoffs between proliferation and transmission in virus evolution- insights from evolutionary and functional analyses of SARS-CoV-2. Virol J 2025; 22:107. [PMID: 40253323 PMCID: PMC12008902 DOI: 10.1186/s12985-025-02727-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2025] [Accepted: 04/07/2025] [Indexed: 04/21/2025] Open
Abstract
To be successful, a virus must maintain high between-host transmissibility while also effectively adapting within hosts. The impact of these potentially conflicting demands on viral genetic diversity and adaptation remains largely unexplored. These modes of adaptation can induce uncorrelated selection, bring mutations that enhance certain fitness aspects at the expense of others to high freqency, and contribute to the maintenance of genetic variation. The vast wealth of SARS-CoV-2 genetic data gathered from within and across hosts offers an unparalleled opportunity to test the above hypothesis. By analyzing a large set of SARS-CoV-2 sequences (~ 2 million) collected from early 2020 to mid-2021, we found that high frequency mutations within hosts are sometimes detrimental during between-host transmission. This highlights potential inverse selection pressures within- versus between-hosts. We also identified a group of nonsynonymous changes likely maintained by pleiotropy, as their frequencies are significantly higher than neutral expectation, yet they have never experienced clonal expansion. Analyzing one such mutation, spike M1237I, reveals that spike I1237 boosts viral assembly but reduces in vitro transmission, highlighting its pleiotropic effect. Though they make up about 2% of total changes, these types of variants represent 37% of SARS-CoV-2 genetic diversity. These mutations are notably prevalent in the Omicron variant from late 2021, hinting that pleiotropy may promote positive epistasis and new successful variants. Estimates of viral population dynamics, such as population sizes and transmission bottlenecks, assume neutrality of within-host variation. Our demonstration that these changes may affect fitness calls into question the robustness of these estimates.
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Affiliation(s)
- Jui-Hung Tai
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, 10002, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan
| | - Ding-Chin Lee
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10617, Taiwan
| | - Hsin-Fu Lin
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, 10002, Taiwan
| | - Tai-Ling Chao
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, 10002, Taiwan
| | - Yongsen Ruan
- State Key Laboratory of Biocontrol, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Ya-Wen Cheng
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10617, Taiwan
| | - Yu-Chi Chou
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan
| | - You-Yu Lin
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, 10002, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan
| | - Sui-Yuan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, 10002, Taiwan
| | - Pei-Jer Chen
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, 10002, Taiwan
- Hepatitis Research Center, National Taiwan University College of Medicine and National Taiwan University Hospital, Taipei, 10002, Taiwan
- Department of Internal Medicine, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, 10002, Taiwan
- Department of Medical Research, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, 10002, Taiwan
| | - Shiou-Hwei Yeh
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10617, Taiwan.
| | - Hurng-Yi Wang
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, 10002, Taiwan.
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan.
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 10617, Taiwan.
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, 10002, Taiwan.
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3
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Ali S, Giovanetti M, Johnston C, Urdaneta-Páez V, Azarian T, Cella E. From Emergence to Evolution: Dynamics of the SARS-CoV-2 Omicron Variant in Florida. Pathogens 2024; 13:1095. [PMID: 39770354 PMCID: PMC11679505 DOI: 10.3390/pathogens13121095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Revised: 12/04/2024] [Accepted: 12/10/2024] [Indexed: 01/11/2025] Open
Abstract
The continual evolution of SARS-CoV-2 has significantly influenced the global response to the COVID-19 pandemic, with the emergence of highly transmissible and immune-evasive variants posing persistent challenges. The Omicron variant, first identified in November 2021, rapidly replaced the Delta variant, becoming the predominant strain worldwide. In Florida, Omicron was first detected in December 2021, leading to an unprecedented surge in cases that surpassed all prior waves, despite extensive vaccination efforts. This study investigates the molecular evolution and transmission dynamics of the Omicron lineages during Florida's Omicron waves, supported by a robust dataset of over 1000 sequenced genomes. Through phylogenetic and phylodynamic analyses, we capture the rapid diversification of the Omicron lineages, identifying significant importation events, predominantly from California, Texas, and New York, and exportation to North America, Europe, and South America. Variants such as BA.1, BA.2, BA.4, and BA.5 exhibited distinct transmission patterns, with BA.2 showing the ability to reinfect individuals previously infected with BA.1. Despite the high transmissibility and immune evasion of the Omicron sub-lineages, the plateauing of cases by late 2022 suggests increasing population immunity from prior infection and vaccination. Our findings underscore the importance of continuous genomic surveillance in identifying variant introductions, mapping transmission pathways, and guiding public health interventions to mitigate current and future pandemic risks.
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Affiliation(s)
- Sobur Ali
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA; (S.A.); (C.J.); (V.U.-P.)
| | - Marta Giovanetti
- Department of Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, 00128 Roma, Italy;
- Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Minas Gerais 30190-009, Brazil
- Climate Amplified Diseases and Epidemics (CLIMADE)—CLIMADE Americas, Belo Horizonte 30190-002, Brazil
| | - Catherine Johnston
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA; (S.A.); (C.J.); (V.U.-P.)
| | - Verónica Urdaneta-Páez
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA; (S.A.); (C.J.); (V.U.-P.)
| | - Taj Azarian
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA; (S.A.); (C.J.); (V.U.-P.)
| | - Eleonora Cella
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA; (S.A.); (C.J.); (V.U.-P.)
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She B, Smith RL, Pytlarz I, Sundaram S, Paré PE. A framework for counterfactual analysis, strategy evaluation, and control of epidemics using reproduction number estimates. PLoS Comput Biol 2024; 20:e1012569. [PMID: 39565799 PMCID: PMC11616887 DOI: 10.1371/journal.pcbi.1012569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 12/04/2024] [Accepted: 10/17/2024] [Indexed: 11/22/2024] Open
Abstract
During pandemics, countries, regions, and communities develop various epidemic models to evaluate spread and guide mitigation policies. However, model uncertainties caused by complex transmission behaviors, contact-tracing networks, time-varying parameters, human factors, and limited data present significant challenges to model-based approaches. To address these issues, we propose a novel framework that centers around reproduction number estimates to perform counterfactual analysis, strategy evaluation, and feedback control of epidemics. The framework 1) introduces a mechanism to quantify the impact of the testing-for-isolation intervention strategy on the basic reproduction number. Building on this mechanism, the framework 2) proposes a method to reverse engineer the effective reproduction number under different strengths of the intervention strategy. In addition, based on the method that quantifies the impact of the testing-for-isolation strategy on the basic reproduction number, the framework 3) proposes a closed-loop control algorithm that uses the effective reproduction number both as feedback to indicate the severity of the spread and as the control goal to guide adjustments in the intensity of the intervention. We illustrate the framework, along with its three core methods, by addressing three key questions and validating its effectiveness using data collected during the COVID-19 pandemic at the University of Illinois Urbana-Champaign (UIUC) and Purdue University: 1) How severe would an outbreak have been without the implemented intervention strategies? 2) What impact would varying the intervention strength have had on an outbreak? 3) How can we adjust the intervention intensity based on the current state of an outbreak?
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Affiliation(s)
- Baike She
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Rebecca Lee Smith
- Department of Pathobiology, University of Illinois Urbana-Champaign, Champaign, Illinois, United States of America
| | - Ian Pytlarz
- Institutional Data Analytics + Assessment, Purdue University, West Lafayette, Indiana, United States of America
| | - Shreyas Sundaram
- Elmore Family School of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Philip E. Paré
- Elmore Family School of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana, United States of America
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Fang FF. As the virus evolves, so too must we: a drug developer's perspective : We need a new paradigm in searching for next-generation countermeasures. Virol J 2022; 19:159. [PMID: 36217145 PMCID: PMC9549815 DOI: 10.1186/s12985-022-01887-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/13/2022] [Indexed: 11/26/2022] Open
Abstract
The SARS-CoV-2 virus has been raging globally for over 2 years with no end in sight. It has become clear that this virus possesses enormous genetic plasticity, and it will not be eradicated. Under increasing selective pressure from population immunity, the evolution of SARS-CoV-2 has driven it towards greater infectivity, and evasion of humoral and cellular immunity. Omicron and its expanding army of subvariants and recombinants have impaired vaccine protection and made most antibody drugs obsolete. Antiviral drugs, though presently effective, may select for more resistant strains over time. It may be inevitable, then, that future SARS-CoV-2 variants will be immune to our current virus-directed countermeasures. Thus, to gain control over the virus, we need to adopt a new paradigm in searching for next-generation countermeasures and develop host-directed therapeutics (HDTx) and host-directed antivirals (HDA). Different from the virus-directed countermeasures, HDTx and HDA may offer variant agnostic treatment to reduce the risk and severity of infections. In addition, they may exert more uniform effects against the genetically diverse SARS-CoV-2 quasispecies, thereby diminishing the risk of selecting resistant variants. Some promising HDTx and HDA approaches are summarized here.
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Affiliation(s)
- Fang Flora Fang
- Abimmune Biopharma, Inc., P.O. Box 8793, Rancho Santa Fe, CA, 92037, USA.
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