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Article ; Online: Computational identification of antibody-binding epitopes from mimotope datasets.

Li, Rang / Wilderotter, Sabrina / Stoddard, Madison / Van Egeren, Debra / Chakravarty, Arijit / Joseph-McCarthy, Diane

Frontiers in bioinformatics

2024 Volume 4, Page(s) 1295972

Abstract: Introduction: ...

Abstract	Introduction:
Language	English
Publishing date	2024-02-23
Publishing country	Switzerland
Document type	Journal Article
ISSN	2673-7647
ISSN (online)	2673-7647
DOI	10.3389/fbinf.2024.1295972
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Accuracy of Inferences About the Reproductive Number and Superspreading Potential of SARS-CoV-2 with Incomplete Contact Tracing Data.

Bayly, Henry / Mei, Winnie / Egeren, Debra / Stoddard, Madison / Chakravarty, Arijit / White, Laura F

Research square

2023

Abstract: The basic reproductive number ( ... ...

Abstract	The basic reproductive number (R
Language	English
Publishing date	2023-12-29
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-3760127/v1
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Looking under the lamp-post: quantifying the performance of contact tracing in the United States during the SARS-CoV-2 pandemic.

Bayly, Henry / Stoddard, Madison / Van Egeren, Debra / Murray, Eleanor J / Raifman, Julia / Chakravarty, Arijit / White, Laura F

BMC public health

2024 Volume 24, Issue 1, Page(s) 595

Abstract: Contact tracing forms a crucial part of the public-health toolbox in mitigating and understanding emergent pathogens and nascent disease outbreaks. Contact tracing in the United States was conducted during the pre-Omicron phase of the ongoing COVID-19 ... ...

Abstract	Contact tracing forms a crucial part of the public-health toolbox in mitigating and understanding emergent pathogens and nascent disease outbreaks. Contact tracing in the United States was conducted during the pre-Omicron phase of the ongoing COVID-19 pandemic. This tracing relied on voluntary reporting and responses, often using rapid antigen tests due to lack of accessibility to PCR tests. These limitations, combined with SARS-CoV-2's propensity for asymptomatic transmission, raise the question "how reliable was contact tracing for COVID-19 in the United States"? We answered this question using a Markov model to examine the efficiency with which transmission could be detected based on the design and response rates of contact tracing studies in the United States. Our results suggest that contact tracing protocols in the U.S. are unlikely to have identified more than 1.65% (95% uncertainty interval: 1.62-1.68%) of transmission events with PCR testing and 1.00% (95% uncertainty interval 0.98-1.02%) with rapid antigen testing. When considering a more robust contact tracing scenario, based on compliance rates in East Asia with PCR testing, this increases to 62.7% (95% uncertainty interval: 62.6-62.8%). We did not assume presence of asymptomatic transmission or superspreading, making our estimates upper bounds on the actual percentages traced. These findings highlight the limitations in interpretability for studies of SARS-CoV-2 disease spread based on U.S. contact tracing and underscore the vulnerability of the population to future disease outbreaks, for SARS-CoV-2 and other pathogens.
MeSH term(s)	Humans ; United States/epidemiology ; SARS-CoV-2 ; COVID-19/diagnosis ; COVID-19/epidemiology ; Contact Tracing/methods ; Pandemics ; Disease Outbreaks
Language	English
Publishing date	2024-02-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2041338-5
ISSN	1471-2458 ; 1471-2458
ISSN (online)	1471-2458
ISSN	1471-2458
DOI	10.1186/s12889-024-18012-z
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Antibody escape, the risk of serotype formation, and rapid immune waning: Modeling the implications of SARS-CoV-2 immune evasion.

Albright, Catherine / Van Egeren, Debra / Thakur, Aditya / Chakravarty, Arijit / White, Laura F / Stoddard, Madison

PloS one

2023 Volume 18, Issue 10, Page(s) e0292099

Abstract: As the COVID-19 pandemic progresses, widespread community transmission of SARS-CoV-2 has ushered in a volatile era of viral immune evasion rather than the much-heralded stability of "endemicity" or "herd immunity." At this point, an array of viral ... ...

Abstract	As the COVID-19 pandemic progresses, widespread community transmission of SARS-CoV-2 has ushered in a volatile era of viral immune evasion rather than the much-heralded stability of "endemicity" or "herd immunity." At this point, an array of viral strains has rendered essentially all monoclonal antibody therapeutics obsolete and strongly undermined the impact of vaccinal immunity on SARS-CoV-2 transmission. In this work, we demonstrate that antibody escape resulting in evasion of pre-existing immunity is highly evolutionarily favored and likely to cause waves of short-term transmission. In the long-term, invading strains that induce weak cross-immunity against pre-existing strains may co-circulate with those pre-existing strains. This would result in the formation of serotypes that increase disease burden, complicate SARS-CoV-2 control, and raise the potential for increases in viral virulence. Less durable immunity does not drive positive selection as a trait, but such strains may transmit at high levels if they establish. Overall, our results draw attention to the importance of inter-strain cross-immunity as a driver of transmission trends and the importance of early immune evasion data to predict the trajectory of the pandemic.
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19 ; Immune Evasion ; Pandemics/prevention & control ; Serogroup ; Antibodies, Viral
Chemical Substances	Antibodies, Viral
Language	English
Publishing date	2023-10-18
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0292099
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Structures, activity and mechanism of the Type IIS restriction endonuclease PaqCI.

Kennedy, Madison A / Hosford, Christopher J / Azumaya, Caleigh M / Luyten, Yvette A / Chen, Minyong / Morgan, Richard D / Stoddard, Barry L

Nucleic acids research

2023 Volume 51, Issue 9, Page(s) 4467–4487

Abstract: Type IIS restriction endonucleases contain separate DNA recognition and catalytic domains and cleave their substrates at well-defined distances outside their target sequences. They are employed in biotechnology for a variety of purposes, including the ... ...

Abstract	Type IIS restriction endonucleases contain separate DNA recognition and catalytic domains and cleave their substrates at well-defined distances outside their target sequences. They are employed in biotechnology for a variety of purposes, including the creation of gene-targeting zinc finger and TAL effector nucleases and DNA synthesis applications such as Golden Gate assembly. The most thoroughly studied Type IIS enzyme, FokI, has been shown to require multimerization and engagement with multiple DNA targets for optimal cleavage activity; however, details of how it or similar enzymes forms a DNA-bound reaction complex have not been described at atomic resolution. Here we describe biochemical analyses of DNA cleavage by the Type IIS PaqCI restriction endonuclease and a series of molecular structures in the presence and absence of multiple bound DNA targets. The enzyme displays a similar tetrameric organization of target recognition domains in the absence or presence of bound substrate, with a significant repositioning of endonuclease domains in a trapped DNA-bound complex that is poised to deliver the first of a series of double-strand breaks. PaqCI and FokI share similar structural mechanisms of DNA cleavage, but considerable differences in their domain organization and quaternary architecture, facilitating comparisons between distinct Type IIS enzymes.
MeSH term(s)	Deoxyribonucleases, Type II Site-Specific/chemistry ; Deoxyribonucleases, Type II Site-Specific/metabolism ; DNA/chemistry ; DNA/genetics ; DNA/metabolism ; DNA Breaks, Double-Stranded ; Substrate Specificity
Chemical Substances	Deoxyribonucleases, Type II Site-Specific (EC 3.1.21.4) ; DNA (9007-49-2) ; endodeoxyribonuclease FokI (EC 3.1.21.-)
Language	English
Publishing date	2023-03-24
Publishing country	England
Document type	Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkad228
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Looking under the lamp-post: quantifying the performance of contact tracing in the United States during the SARS-CoV-2 pandemic.

Bayly, Henry / Stoddard, Madison / Egeren, Debra Van / Murray, Eleanor J / Raifman, Julia / Chakravarty, Arijit / White, Laura F

Research square

2023

Abstract	Contact tracing forms a crucial part of the public-health toolbox in mitigating and understanding emergent pathogens and nascent disease outbreaks. Contact tracing in the United States was conducted during the pre-Omicron phase of the ongoing COVID-19 pandemic. This tracing relied on voluntary reporting and responses, often using rapid antigen tests (with a high false negative rate) due to lack of accessibility to PCR tests. These limitations, combined with SARS-CoV-2's propensity for asymptomatic transmission, raise the question "how reliable was contact tracing for COVID-19 in the United States"? We answered this question using a Markov model to examine the efficiency with which transmission could be detected based on the design and response rates of contact tracing studies in the United States. Our results suggest that contact tracing protocols in the U.S. are unlikely to have identified more than 1.65% (95% uncertainty interval: 1.62%-1.68%) of transmission events with PCR testing and 0.88% (95% uncertainty interval 0.86%-0.89%) with rapid antigen testing. When considering an optimal scenario, based on compliance rates in East Asia with PCR testing, this increases to 62.7% (95% uncertainty interval: 62.6%-62.8%). These findings highlight the limitations in interpretability for studies of SARS-CoV-2 disease spread based on U.S. contact tracing and underscore the vulnerability of the population to future disease outbreaks, for SARS-CoV-2 and other pathogens.
Language	English
Publishing date	2023-06-06
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-2953875/v1
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Stepwise design of pseudosymmetric protein hetero-oligomers.

Kibler, Ryan D / Lee, Sangmin / Kennedy, Madison A / Wicky, Basile I M / Lai, Stella M / Kostelic, Marius M / Li, Xinting / Chow, Cameron M / Carter, Lauren / Wysocki, Vicki H / Stoddard, Barry L / Baker, David

bioRxiv : the preprint server for biology

2023

Abstract: Pseudosymmetric hetero-oligomers with three or more unique subunits with overall structural (but not sequence) symmetry play key roles in biology, and systematic approaches for generating such ... ...

Abstract	Pseudosymmetric hetero-oligomers with three or more unique subunits with overall structural (but not sequence) symmetry play key roles in biology, and systematic approaches for generating such proteins
Language	English
Publishing date	2023-04-07
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.04.07.535760
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The gray swan: model-based assessment of the risk of sudden failure of hybrid immunity to SARS-CoV-2

Stoddard, Madison / Yuan, Lin / Sarkar, Sharanya / Van Egeren, Debra / White, Laura / Chakravarty, Arijit

medRxiv

Abstract: In the fourth year of the COVID-19 pandemic, public health authorities worldwide have adopted a strategy of learning to live with SARS-CoV-2. This has involved the removal of measures for limiting viral spread, resulting in a large burden of recurrent ... ...

Abstract	In the fourth year of the COVID-19 pandemic, public health authorities worldwide have adopted a strategy of learning to live with SARS-CoV-2. This has involved the removal of measures for limiting viral spread, resulting in a large burden of recurrent SARS-CoV-2 infections. Crucial for managing this burden is the concept of the so-called wall of hybrid immunity, through repeated reinfections and vaccine boosters, to reduce the risk of severe disease and death. Protection against both infection and severe disease is provided by the induction of neutralizing antibodies (nAbs) against SARS-CoV-2. However, pharmacokinetic (PK) waning and rapid viral evolution both degrade nAb binding titers. The recent emergence of variants with strongly immune evasive potential against both the vaccinal and natural immune responses raises the question of whether the wall of population-level immunity can be maintained in the face of large jumps in nAb binding potency. Here we use an agent-based simulation to address this question. Our findings suggest large jumps in viral evolution may cause failure of population immunity resulting in sudden increases in mortality. As a rise in mortality will only become apparent in the weeks following a wave of disease, reactive public health strategies will not be able to provide meaningful risk mitigation. Learning to live with the virus could thus lead to large death tolls with very little warning. Our work points to the importance of proactive management strategies for the ongoing pandemic, and to the need for multifactorial approaches to COVID-19 disease control.
Keywords	covid19
Language	English
Publishing date	2023-03-01
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2023.02.26.23286471
Database	COVID19

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Article ; Online: Antibody escape, the risk of serotype formation, and rapid immune waning: modeling the implications of SARS-CoV-2 immune evasion

Albright, Catherine / Van Egeren, Debra / Thakur, Aditya / Chakravarty, Arijit / White, Laura / Stoddard, Madison

medRxiv

Abstract	As the COVID-19 pandemic progresses, widespread community transmission of SARS-CoV-2 has ushered in a volatile era of viral immune evasion rather than the much-heralded stability of "endemicity" or "herd immunity." At this point, an array of viral variants has rendered essentially all monoclonal antibody therapeutics obsolete and strongly undermined the impact of vaccinal immunity on SARS-CoV-2 transmission. In this work, we demonstrate that antigenic drift resulting in evasion of pre-existing immunity is highly evolutionarily favored and likely to cause waves of short-term transmission. In the long-term, invading variants that induce weak cross-immunity against pre-existing strains may co-circulate with those pre-existing strains. This would result in the formation of serotypes that increase disease burden, complicate SARS-CoV-2 control and raise the potential for increases in viral virulence. Less durable immunity does not drive positive selection as a trait, but such strains may transmit at high levels if they establish. Overall, our results draw attention to the importance of inter-strain cross-immunity as a driver of transmission trends and the importance of early immune evasion data to predict the trajectory of the pandemic.
Keywords	covid19
Language	English
Publishing date	2023-01-26
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2023.01.25.23285031
Database	COVID19

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Article ; Online: Using translational in vitro-in vivo modeling to improve drug repurposing outcomes for inhaled COVID-19 therapeutics

Stoddard, Madison / Yuan, Lin / Chakravarty, Arijit

medRxiv

Abstract: The ongoing COVID-19 pandemic has created an urgent need for antiviral treatments that can be deployed rapidly. Drug repurposing represents a promising means of achieving this objective, but repurposing efforts are often unsuccessful. A common hurdle to ... ...

Abstract	The ongoing COVID-19 pandemic has created an urgent need for antiviral treatments that can be deployed rapidly. Drug repurposing represents a promising means of achieving this objective, but repurposing efforts are often unsuccessful. A common hurdle to effective drug repurposing is a failure to achieve a sufficient therapeutic window in the new indication. A clear example is the use of ivermectin in COVID-19, where the approved dose (administered orally) fails to achieve therapeutic concentrations in the lungs. Our proposed solution to the problem of ineffective drug repurposing for COVID-19 antivirals is two-fold: to broaden the therapeutic window by reformulating therapeutics for the pulmonary route, and to select drug repurposing candidates based on their model-predicted therapeutic index for inhalation. In this article, we propose a two-stage model-driven screening and validation process for selecting inhaled antiviral drug repurposing candidates. While we have applied this approach in the specific context of COVID-19, this in vitro-in vivo translational methodology is also broadly applicable to repurposing drugs for diseases of the lower respiratory tract.
Keywords	covid19
Language	English
Publishing date	2021-03-12
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.03.11.21253375
Database	COVID19

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