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Article: Uses and Challenges of Antiviral Polyclonal and Monoclonal Antibody Therapies.

Struble, Evi B / Rawson, Jonathan M O / Stantchev, Tzanko / Scott, Dorothy / Shapiro, Marjorie A

2023 Volume 15, Issue 5

Abstract: Viral diseases represent a major public health concerns and ever-present risks for developing into future pandemics. Antiviral antibody therapeutics, either alone or in combination with other therapies, emerged as valuable preventative and treatment ... ...

Abstract	Viral diseases represent a major public health concerns and ever-present risks for developing into future pandemics. Antiviral antibody therapeutics, either alone or in combination with other therapies, emerged as valuable preventative and treatment options, including during global emergencies. Here we will discuss polyclonal and monoclonal antiviral antibody therapies, focusing on the unique biochemical and physiological properties that make them well-suited as therapeutic agents. We will describe the methods of antibody characterization and potency assessment throughout development, highlighting similarities and differences between polyclonal and monoclonal products as appropriate. In addition, we will consider the benefits and challenges of antiviral antibodies when used in combination with other antibodies or other types of antiviral therapeutics. Lastly, we will discuss novel approaches to the characterization and development of antiviral antibodies and identify areas that would benefit from additional research.
Language	English
Publishing date	2023-05-19
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2527217-2
ISSN	1999-4923
ISSN	1999-4923
DOI	10.3390/pharmaceutics15051538
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Article ; Online: Development of a Cell-Based Luciferase Complementation Assay for Identification of SARS-CoV-2 3CL

Rawson, Jonathan M O / Duchon, Alice / Nikolaitchik, Olga A / Pathak, Vinay K / Hu, Wei-Shau

Viruses

2021 Volume 13, Issue 2

Abstract: The 3C-like protease ( ... ...

Abstract	The 3C-like protease (3CL
MeSH term(s)	Antiviral Agents/metabolism ; Antiviral Agents/pharmacology ; Cell Survival/drug effects ; Coronavirus 3C Proteases/antagonists & inhibitors ; Coronavirus 3C Proteases/genetics ; Coronavirus 3C Proteases/metabolism ; Drug Evaluation, Preclinical ; HEK293 Cells ; Humans ; Lentivirus/genetics ; Luciferases/genetics ; Luciferases/metabolism ; Protease Inhibitors/metabolism ; Protease Inhibitors/pharmacology ; SARS-CoV-2/enzymology
Chemical Substances	Antiviral Agents ; Protease Inhibitors ; Luciferases (EC 1.13.12.-) ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
Language	English
Publishing date	2021-01-24
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v13020173
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Article ; Online: Evaluation of SARS-CoV-2 RNA Rebound After Nirmatrelvir/Ritonavir Treatment in Randomized, Double-Blind, Placebo-Controlled Trials - United States and International Sites, 2021-2022.

Harrington, Patrick R / Cong, Jie / Troy, Stephanie B / Rawson, Jonathan M O / O'Rear, Julian J / Valappil, Thamban Illath / McGarry Connelly, Sarah / Farley, John / Birnkrant, Debra

MMWR. Morbidity and mortality weekly report

2023 Volume 72, Issue 51, Page(s) 1365–1370

Abstract: Rebound of SARS-CoV-2 shedding or COVID-19 signs and symptoms has been described after treatment with nirmatrelvir/ritonavir (Paxlovid). The direct association of nirmatrelvir/ritonavir to COVID-19 rebound remains unclear because most reports are based ... ...

Abstract	Rebound of SARS-CoV-2 shedding or COVID-19 signs and symptoms has been described after treatment with nirmatrelvir/ritonavir (Paxlovid). The direct association of nirmatrelvir/ritonavir to COVID-19 rebound remains unclear because most reports are based on individual cases or nonrandomized studies. Viral RNA shedding data from two phase 2/3, randomized, double-blind, placebo-controlled clinical trials of nirmatrelvir/ritonavir (Evaluation of Protease Inhibition for COVID-19 in High-Risk Patients [EPIC-HR] and Evaluation of Protease Inhibition for COVID-19 in Standard-Risk Patients [EPIC-SR]) were analyzed to investigate the role of nirmatrelvir/ritonavir treatment in COVID-19 rebound. Rates of rebound of SARS-CoV-2 RNA shedding, identified based on an increase in nasopharyngeal viral RNA levels from day 5 (end-of-treatment) to day 10 or day 14, were similar between nirmatrelvir/ritonavir and placebo recipients. Among subjects with a virologic response through day 5, viral RNA rebound occurred in 6.4%-8.4% of nirmatrelvir/ritonavir recipients and 5.9%-6.5% of placebo recipients across EPIC-HR and the 2021/pre-Omicron and 2022/Omicron enrollment periods of EPIC-SR. Viral RNA rebound after nirmatrelvir/ritonavir treatment was not associated with COVID-19-related hospitalization or death. Data from randomized trials demonstrated that SARS-CoV-2 rebound can occur with or without antiviral treatment, supporting the Food and Drug Administration's determination of safety and efficacy of nirmatrelvir/ritonavir in eligible patients at high risk for severe COVID-19.
MeSH term(s)	Humans ; Antiviral Agents/therapeutic use ; COVID-19 ; COVID-19 Drug Treatment ; Peptide Hydrolases ; Ritonavir/therapeutic use ; RNA, Viral ; SARS-CoV-2 ; Randomized Controlled Trials as Topic
Chemical Substances	Antiviral Agents ; nirmatrelvir (7R9A5P7H32) ; nirmatrelvir and ritonavir drug combination ; Peptide Hydrolases (EC 3.4.-) ; Ritonavir (O3J8G9O825) ; RNA, Viral
Language	English
Publishing date	2023-12-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	412775-4
ISSN	1545-861X ; 0149-2195
ISSN (online)	1545-861X
ISSN	0149-2195
DOI	10.15585/mmwr.mm7251a2
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Article ; Online: Transcription Start Site Heterogeneity and Preferential Packaging of Specific Full-Length RNA Species Are Conserved Features of Primate Lentiviruses.

Rawson, Jonathan M O / Nikolaitchik, Olga A / Shakya, Saurabh / Keele, Brandon F / Pathak, Vinay K / Hu, Wei-Shau

Microbiology spectrum

2022 Volume 10, Issue 4, Page(s) e0105322

Abstract: ... related to the progenitor virus that gave rise to HIV-1 group M, the pandemic pathogen, exhibited TSS ...

Abstract	HIV-1 must package its RNA genome to generate infectious viruses. Recent studies have revealed that during genome packaging, HIV-1 not only excludes cellular mRNAs, but also distinguishes among full-length viral RNAs. Using NL4-3 and MAL molecular clones, multiple transcription start sites (TSS) were identified, which generate full-length RNAs that differ by only a few nucleotides at the 5' end. However, HIV-1 selectively packages RNAs containing one guanosine (1G RNA) over RNAs with three guanosines (3G RNA) at the 5' end. Thus, the 5' context of HIV-1 full-length RNA can affect its function. To determine whether the regulation of genome packaging by TSS usage is unique to NL4-3 and MAL, we examined 15 primate lentiviruses including transmitted founder viruses of HIV-1, HIV-2, and several simian immunodeficiency viruses (SIVs). We found that all 15 viruses used multiple TSS to some extent. However, the level of TSS heterogeneity in infected cells varied greatly, even among closely related viruses belonging to the same subtype. Most viruses also exhibited selective packaging of specific full-length viral RNA species into particles. These findings demonstrate that TSS heterogeneity and selective packaging of certain full-length viral RNA species are conserved features of primate lentiviruses. In addition, an SIV strain closely related to the progenitor virus that gave rise to HIV-1 group M, the pandemic pathogen, exhibited TSS usage similar to some HIV-1 strains and preferentially packaged 1G RNA. These findings indicate that multiple TSS usage and selective packaging of a particular unspliced RNA species predate the emergence of HIV-1.
MeSH term(s)	Animals ; HIV-1/genetics ; Lentiviruses, Primate/genetics ; RNA, Viral/genetics ; Transcription Initiation Site ; Virion/genetics
Chemical Substances	RNA, Viral
Language	English
Publishing date	2022-06-23
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.01053-22
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Article ; Online: HIV-1 usurps transcription start site heterogeneity of host RNA polymerase II to maximize replication fitness.

Nikolaitchik, Olga A / Islam, Saiful / Kitzrow, Jonathan P / Duchon, Alice / Cheng, Zetao / Liu, Yang / Rawson, Jonathan M O / Shao, Wei / Nikolaitchik, Maria / Kearney, Mary F / Maldarelli, Frank / Musier-Forsyth, Karin / Pathak, Vinay K / Hu, Wei-Shau

Proceedings of the National Academy of Sciences of the United States of America

2023 Volume 120, Issue 23, Page(s) e2305103120

Abstract: HIV-1 relies on host RNA polymeraseII (Pol II) to transcribe its genome and uses multiple transcription start sites (TSS), including three consecutive guanosines located near the U3-R junction, to generate transcripts containing three, two, and one ... ...

Abstract	HIV-1 relies on host RNA polymeraseII (Pol II) to transcribe its genome and uses multiple transcription start sites (TSS), including three consecutive guanosines located near the U3-R junction, to generate transcripts containing three, two, and one guanosine at the 5' end, referred to as 3G, 2G, and 1G RNA, respectively. The 1G RNA is preferentially selected for packaging, indicating that these 99.9% identical RNAs exhibit functional differences and highlighting the importance of TSS selection. Here, we demonstrate that TSS selection is regulated by sequences between the CATA/TATA box and the beginning of R. Furthermore, we have generated two HIV-1 mutants with distinct 2-nucleotide modifications that predominantly express 3G RNA or 1G RNA. Both mutants can generate infectious viruses and undergo multiple rounds of replication in T cells. However, both mutants exhibit replication defects compared to the wild-type virus. The 3G-RNA-expressing mutant displays an RNA genome-packaging defect and delayed replication kinetics, whereas the 1G-RNA-expressing mutant exhibits reduced Gag expression and a replication fitness defect. Additionally, reversion of the latter mutant is frequently observed, consistent with sequence correction by plus-strand DNA transfer during reverse transcription. These findings demonstrate that HIV-1 maximizes its replication fitness by usurping the TSS heterogeneity of host RNA Pol II to generate unspliced RNAs with different specialized roles in viral replication. The three consecutive guanosines at the junction of U3 and R may also maintain HIV-1 genome integrity during reverse transcription. These studies reveal the intricate regulation of HIV-1 RNA and complex replication strategy.
MeSH term(s)	RNA Polymerase II/genetics ; RNA Polymerase II/metabolism ; HIV-1/physiology ; Transcription Initiation Site ; RNA, Viral/genetics ; RNA, Viral/metabolism ; Virus Replication/genetics
Chemical Substances	RNA Polymerase II (EC 2.7.7.-) ; RNA, Viral
Language	English
Publishing date	2023-05-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2305103120
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Article ; Online: Selective packaging of HIV-1 RNA genome is guided by the stability of 5' untranslated region polyA stem.

Nikolaitchik, Olga A / Liu, Shuohui / Kitzrow, Jonathan P / Liu, Yang / Rawson, Jonathan M O / Shakya, Saurabh / Cheng, Zetao / Pathak, Vinay K / Hu, Wei-Shau / Musier-Forsyth, Karin

Proceedings of the National Academy of Sciences of the United States of America

2021 Volume 118, Issue 50

Abstract: To generate infectious virus, HIV-1 must package two copies of its full-length RNA into particles. HIV-1 transcription initiates from multiple, neighboring sites, generating RNA species that only differ by a few nucleotides at the 5' end, including those ...

Abstract	To generate infectious virus, HIV-1 must package two copies of its full-length RNA into particles. HIV-1 transcription initiates from multiple, neighboring sites, generating RNA species that only differ by a few nucleotides at the 5' end, including those with one (1G) or three (3G) 5' guanosines. Strikingly, 1G RNA is preferentially packaged into virions over 3G RNA. We investigated how HIV-1 distinguishes between these nearly identical RNAs using in-gel chemical probing combined with recently developed computational tools for determining RNA conformational ensembles, as well as cell-based assays to quantify the efficiency of RNA packaging into viral particles. We found that 1G and 3G RNAs fold into distinct structural ensembles. The 1G RNA, but not the 3G RNA, primarily adopts conformations with an intact polyA stem, exposed dimerization initiation site, and multiple, unpaired guanosines known to mediate Gag binding. Furthermore, we identified mutants that exhibited altered genome selectivity and packaged 3G RNA efficiently. In these mutants, both 1G and 3G RNAs fold into similar conformational ensembles, such that they can no longer be distinguished. Our findings demonstrate that polyA stem stability guides RNA-packaging selectivity. These studies also uncover the mechanism by which HIV-1 selects its genome for packaging: 1G RNA is preferentially packaged because it exposes structural elements that promote RNA dimerization and Gag binding.
MeSH term(s)	5' Untranslated Regions/physiology ; Genome, Viral ; HEK293 Cells ; HIV-1/physiology ; Humans ; RNA, Viral/metabolism ; Transcription Initiation Site ; Virus Assembly/physiology
Chemical Substances	5' Untranslated Regions ; RNA, Viral
Language	English
Publishing date	2021-12-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2114494118
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Article ; Online: Adaptation of HIV-1/HIV-2 Chimeras with Defects in Genome Packaging and Viral Replication.

Rawson, Jonathan M O / Nikolaitchik, Olga A / Yoo, Jennifer A / Somoulay, Xayathed / Brown, Matthew A / Mbuntcha Bogni, Franck S / Pathak, Vinay K / Soheilian, Ferri / Slack, Ryan L / Sarafianos, Stefan G / Hu, Wei-Shau

mBio

2022 Volume 13, Issue 5, Page(s) e0222022

Abstract: Frequent recombination is a hallmark of retrovirus replication. In rare cases, recombination occurs between distantly related retroviruses, generating novel viruses that may significantly impact viral evolution and public health. These recombinants may ... ...

Abstract	Frequent recombination is a hallmark of retrovirus replication. In rare cases, recombination occurs between distantly related retroviruses, generating novel viruses that may significantly impact viral evolution and public health. These recombinants may initially have substantial replication defects due to impaired interactions between proteins and/or nucleic acids from the two parental viruses. However, given the high mutation rates of retroviruses, these recombinants may be able to evolve improved compatibility of these viral elements. To test this hypothesis, we examined the adaptation of chimeras between two distantly related human pathogens: HIV-1 and HIV-2. We constructed HIV-1-based chimeras containing the HIV-2 nucleocapsid (NC) domain of Gag or the two zinc fingers of HIV-2 NC, which are critical for specific recognition of viral RNA. These chimeras exhibited significant defects in RNA genome packaging and replication kinetics in T cells. However, in some experiments, the chimeric viruses replicated with faster kinetics when repassaged, indicating that viral adaptation had occurred. Sequence analysis revealed the acquisition of a single amino acid substitution, S18L, in the first zinc finger of HIV-2 NC. This substitution, which represents a switch from a conserved HIV-2 residue to a conserved HIV-1 residue at this position, partially rescued RNA packaging and replication kinetics. Further analysis revealed that the combination of two substitutions in HIV-2 NC, W10F and S18L, almost completely restored RNA packaging and replication kinetics. Our study demonstrates that chimeras of distantly related retroviruses can adapt and significantly enhance their replication by acquiring a single substitution.
MeSH term(s)	Humans ; HIV-1/metabolism ; HIV-2/genetics ; RNA, Viral/metabolism ; Chimera/metabolism ; Amino Acid Sequence ; Virus Replication ; Viral Proteins/metabolism ; Virus Assembly ; Genome, Viral
Chemical Substances	RNA, Viral ; Viral Proteins
Language	English
Publishing date	2022-08-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, N.I.H., Extramural
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mbio.02220-22
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Article ; Online: Rapid Determination of HIV-1 Mutant Frequencies and Mutation Spectra Using an mCherry/EGFP Dual-Reporter Viral Vector.

Rawson, Jonathan M O / Clouser, Christine L / Mansky, Louis M

Methods in molecular biology (Clifton, N.J.)

2015 Volume 1354, Page(s) 71–88

Abstract: The high mutation rate of human immunodeficiency virus type-1 (HIV-1) has been a pivotal factor in its evolutionary success as a human pathogen, driving the emergence of drug resistance, immune system escape, and invasion of distinct anatomical ... ...

Abstract	The high mutation rate of human immunodeficiency virus type-1 (HIV-1) has been a pivotal factor in its evolutionary success as a human pathogen, driving the emergence of drug resistance, immune system escape, and invasion of distinct anatomical compartments. Extensive research has focused on understanding how various cellular and viral factors alter the rates and types of mutations produced during viral replication. Here, we describe a single-cycle dual-reporter vector assay that relies upon the detection of mutations that eliminate either expression of mCherry or enhanced green fluorescent protein (EGFP). The reporter-based method can be used to efficiently quantify changes in mutant frequencies and mutation spectra that arise due to a variety of factors, including viral mutagens, drug resistance mutations, cellular physiology, and APOBEC3 proteins.
MeSH term(s)	Cell Culture Techniques/methods ; Cell Line ; DNA, Viral/genetics ; DNA, Viral/isolation & purification ; Fluorescent Dyes/metabolism ; Genes, Reporter ; Genetic Vectors/genetics ; Green Fluorescent Proteins/genetics ; HIV Infections/virology ; HIV-1/genetics ; Humans ; Luminescent Proteins/genetics ; Mutation ; Mutation Rate ; Reverse Transcriptase Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/methods ; Red Fluorescent Protein
Chemical Substances	DNA, Viral ; Fluorescent Dyes ; Luminescent Proteins ; enhanced green fluorescent protein ; Green Fluorescent Proteins (147336-22-9)
Language	English
Publishing date	2015-12-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-3046-3_6
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Article ; Online: HIV-1 uncoats in the nucleus near sites of integration.

Burdick, Ryan C / Li, Chenglei / Munshi, MohamedHusen / Rawson, Jonathan M O / Nagashima, Kunio / Hu, Wei-Shau / Pathak, Vinay K

Proceedings of the National Academy of Sciences of the United States of America

2020 Volume 117, Issue 10, Page(s) 5486–5493

Abstract: HIV-1 capsid core disassembly (uncoating) must occur before integration of viral genomic DNA into the host chromosomes, yet remarkably, the timing and cellular location of uncoating is unknown. Previous studies have proposed that intact viral cores are ... ...

Abstract	HIV-1 capsid core disassembly (uncoating) must occur before integration of viral genomic DNA into the host chromosomes, yet remarkably, the timing and cellular location of uncoating is unknown. Previous studies have proposed that intact viral cores are too large to fit through nuclear pores and uncoating occurs in the cytoplasm in coordination with reverse transcription or at the nuclear envelope during nuclear import. The capsid protein (CA) content of the infectious viral cores is not well defined because methods for directly labeling and quantifying the CA in viral cores have been unavailable. In addition, it has been difficult to identify the infectious virions because only one of ∼50 virions in infected cells leads to productive infection. Here, we developed methods to analyze HIV-1 uncoating by direct labeling of CA with GFP and to identify infectious virions by tracking viral cores in living infected cells through viral DNA integration and proviral DNA transcription. Astonishingly, our results show that intact (or nearly intact) viral cores enter the nucleus through a mechanism involving interactions with host protein cleavage and polyadenylation specificity factor 6 (CPSF6), complete reverse transcription in the nucleus before uncoating, and uncoat <1.5 h before integration near (<1.5 μm) their genomic integration sites. These results fundamentally change our current understanding of HIV-1 postentry replication events including mechanisms of nuclear import, uncoating, reverse transcription, integration, and evasion of innate immunity.
MeSH term(s)	Active Transport, Cell Nucleus ; Capsid Proteins/analysis ; Capsid Proteins/metabolism ; Cell Nucleus/virology ; Green Fluorescent Proteins/analysis ; HIV Infections/virology ; HIV-1/physiology ; Humans ; Nuclear Pore/metabolism ; Proteolysis ; Virus Integration ; Virus Replication ; Virus Uncoating ; mRNA Cleavage and Polyadenylation Factors/metabolism
Chemical Substances	Capsid Proteins ; cleavage factor Im, human ; mRNA Cleavage and Polyadenylation Factors ; Green Fluorescent Proteins (147336-22-9)
Language	English
Publishing date	2020-02-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1920631117
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Article ; Online: Ligand Chirality Transfer from Solution State to the Crystalline Self-Assemblies in Circularly Polarized Luminescence (CPL) Active Lanthanide Systems.

Caffrey, David F / Gorai, Tumpa / Rawson, Bláithín / Martínez-Calvo, Miguel / Kitchen, Jonathan A / Murray, Niamh S / Kotova, Oxana / Comby, Steve / Peacock, Robert D / Stachelek, Patrycja / Pal, Robert / Gunnlaugsson, Thorfinnur

Advanced science (Weinheim, Baden-Wurttemberg, Germany)

2024 , Page(s) e2307448

Abstract: The synthesis of a family of chiral and enantiomerically pure pyridyl-diamide (pda) ligands that upon complexation with europium [Eu( ... ...

Abstract	The synthesis of a family of chiral and enantiomerically pure pyridyl-diamide (pda) ligands that upon complexation with europium [Eu(CF
Language	English
Publishing date	2024-03-06
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2808093-2
ISSN	2198-3844 ; 2198-3844
ISSN (online)	2198-3844
ISSN	2198-3844
DOI	10.1002/advs.202307448
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