Madison Stoddard
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View article: The Impact of Vaccination Frequency on COVID-19 Public Health Outcomes: A Model-Based Analysis
The Impact of Vaccination Frequency on COVID-19 Public Health Outcomes: A Model-Based Analysis Open
Background: While the rapid deployment of SARS-CoV-2 vaccines had a significant impact on the ongoing COVID-19 pandemic, rapid viral immune evasion and waning neutralizing antibody titers have degraded vaccine efficacy. Nevertheless, vacci…
View article: Computational identification of antibody-binding epitopes from mimotope datasets
Computational identification of antibody-binding epitopes from mimotope datasets Open
Introduction: A fundamental challenge in computational vaccinology is that most B-cell epitopes are conformational and therefore hard to predict from sequence alone. Another significant challenge is that a great deal of the amino acid sequ…
View article: Accuracy of Inferences About the Reproductive Number and Superspreading Potential of SARS-CoV-2 with Incomplete Contact Tracing Data
Accuracy of Inferences About the Reproductive Number and Superspreading Potential of SARS-CoV-2 with Incomplete Contact Tracing Data Open
The basic reproductive number (R 0 ) and superspreading potential ( k ) are key epidemiological parameters that inform our understanding of a disease’s transmission. Often these values are estimated using the data obtained from contact tra…
View article: COMPUTATIONAL IDENTIFICATION OF ANTIBODY-BINDING EPITOPES FROM MIMOTOPE DATASETS
COMPUTATIONAL IDENTIFICATION OF ANTIBODY-BINDING EPITOPES FROM MIMOTOPE DATASETS Open
A fundamental challenge in computational vaccinology is that most B-cell epitopes are conformational and therefore hard to predict from sequence alone. Another significant challenge is that a great deal of the amino acid sequence of a vira…
View article: Antibody escape, the risk of serotype formation, and rapid immune waning: Modeling the implications of SARS-CoV-2 immune evasion
Antibody escape, the risk of serotype formation, and rapid immune waning: Modeling the implications of SARS-CoV-2 immune evasion Open
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 …
View article: Looking under the lamp-post: quantifying the performance of contact tracing in the United States during the SARS-CoV-2 pandemic
Looking under the lamp-post: quantifying the performance of contact tracing in the United States during the SARS-CoV-2 pandemic Open
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 ongo…
View article: Vaccines Alone Cannot Slow the Evolution of SARS-CoV-2
Vaccines Alone Cannot Slow the Evolution of SARS-CoV-2 Open
The rapid emergence of immune-evading viral variants of SARS-CoV-2 calls into question the practicality of a vaccine-only public-health strategy for managing the ongoing COVID-19 pandemic. It has been suggested that widespread vaccination …
View article: Heterogeneity in Vaccinal Immunity to SARS-CoV-2 Can Be Addressed by a Personalized Booster Strategy
Heterogeneity in Vaccinal Immunity to SARS-CoV-2 Can Be Addressed by a Personalized Booster Strategy Open
SARS-CoV-2 vaccinations were initially shown to substantially reduce risk of severe disease and death. However, pharmacokinetic (PK) waning and rapid viral evolution degrade neutralizing antibody (nAb) binding titers, causing loss of vacci…
View article: Looking under the lamp-post: quantifying the performance of contact tracing in the United States during the SARS-CoV-2 pandemic
Looking under the lamp-post: quantifying the performance of contact tracing in the United States during the SARS-CoV-2 pandemic Open
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 ongo…
View article: The gray swan: model-based assessment of the risk of sudden failure of hybrid immunity to SARS-CoV-2
The gray swan: model-based assessment of the risk of sudden failure of hybrid immunity to SARS-CoV-2 Open
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 …
View article: Pathways to altered virulence of SARS-CoV-2
Pathways to altered virulence of SARS-CoV-2 Open
The recently emerged SARS-CoV-2 virus has led to a prolonged pandemic characterized by ongoing viral evolution. Vaccines have been an important piece in the strategy to combat the virus but have been insufficient to contain it as the virus…
View article: The impact of vaccination frequency on COVID-19 public health outcomes: A model-based analysis
The impact of vaccination frequency on COVID-19 public health outcomes: A model-based analysis Open
While the rapid deployment of SARS-CoV-2 vaccines had a significant impact on the ongoing COVID-19 pandemic, rapid viral immune evasion and waning neutralizing antibody titers have degraded vaccine efficacy. Nevertheless, vaccine manufactu…
View article: Antibody escape, the risk of serotype formation, and rapid immune waning: modeling the implications of SARS-CoV-2 immune evasion
Antibody escape, the risk of serotype formation, and rapid immune waning: modeling the implications of SARS-CoV-2 immune evasion Open
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 …
View article: Shielding under endemic SARS-CoV-2 conditions is easier said than done: a model-based analysis
Shielding under endemic SARS-CoV-2 conditions is easier said than done: a model-based analysis Open
As the COVID-19 pandemic continues unabated, many governments and public-health bodies worldwide have ceased to implement concerted measures for limiting viral spread, placing the onus instead on the individual. In this paper, we examine t…
View article: No magic bullet: Limiting in-school transmission in the face of variable SARS-CoV-2 viral loads
No magic bullet: Limiting in-school transmission in the face of variable SARS-CoV-2 viral loads Open
In the face of a long-running pandemic, understanding the drivers of ongoing SARS-CoV-2 transmission is crucial for the rational management of COVID-19 disease burden. Keeping schools open has emerged as a vital societal imperative during …
View article: Endemicity Is Not a Victory: The Unmitigated Downside Risks of Widespread SARS-CoV-2 Transmission
Endemicity Is Not a Victory: The Unmitigated Downside Risks of Widespread SARS-CoV-2 Transmission Open
The strategy of relying solely on current SARS-CoV-2 vaccines to halt SARS-CoV-2 transmission has proven infeasible. In response, many public-health authorities have advocated for using vaccines to limit mortality while permitting unchecke…
View article: Vaccines alone cannot slow the evolution of SARS-CoV-2
Vaccines alone cannot slow the evolution of SARS-CoV-2 Open
The rapid emergence of immune-evading viral variants of SARS-CoV-2 calls into question the practicality of a vaccine-only public health strategy for managing the ongoing COVID-19 pandemic. It has been suggested that widespread vaccination …
View article: Heterogeneity in vaccinal immunity to SARS-CoV-2 can be addressed by a personalized booster strategy
Heterogeneity in vaccinal immunity to SARS-CoV-2 can be addressed by a personalized booster strategy Open
The ongoing COVID-19 pandemic has placed an unprecedented burden on global health. Crucial for managing this burden, the existing SARS-CoV-2 vaccines have substantially reduced the risk of severe disease and death up to this point. The ind…
View article: No magic bullet: limiting in-school transmission in the face of variable SARS-CoV-2 viral loads
No magic bullet: limiting in-school transmission in the face of variable SARS-CoV-2 viral loads Open
In the face of a long-running pandemic, understanding the drivers of ongoing SARS-CoV-2 transmission is crucial for the rational management of COVID-19 disease burden. Keeping schools open has emerged as a vital societal imperative during …
View article: Endemicity is not a victory: the unmitigated downside risks of widespread SARS-CoV-2 transmission
Endemicity is not a victory: the unmitigated downside risks of widespread SARS-CoV-2 transmission Open
We have entered a new phase of the ongoing COVID-19 pandemic, as the strategy of relying solely on the current SARS-CoV-2 vaccines to bring the pandemic to an end has become infeasible. In response, public-health authorities in many countr…
View article: Rapid relaxation of pandemic restrictions after vaccine rollout favors growth of SARS-CoV-2 variants: A model-based analysis
Rapid relaxation of pandemic restrictions after vaccine rollout favors growth of SARS-CoV-2 variants: A model-based analysis Open
The development and deployment of several SARS-CoV-2 vaccines in a little over a year is an unprecedented achievement of modern medicine. The high levels of efficacy against transmission for some of these vaccines makes it feasible to use …
View article: Beyond the new normal: Assessing the feasibility of vaccine-based suppression of SARS-CoV-2
Beyond the new normal: Assessing the feasibility of vaccine-based suppression of SARS-CoV-2 Open
As the COVID-19 pandemic drags into its second year, there is hope on the horizon, in the form of SARS-CoV-2 vaccines which promise disease suppression and a return to pre-pandemic normalcy. In this study we critically examine the basis fo…
View article: Using mixed-effects modeling to estimate decay kinetics of response to SARS-CoV-2 infection
Using mixed-effects modeling to estimate decay kinetics of response to SARS-CoV-2 infection Open
The duration of natural immunity in response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a matter of some debate in the literature at present. For example, in a recent publication characterizing SARS-CoV-2 immunity o…
View article: The specter of Manaus: the risks of a rapid return to pre-pandemic conditions after COVID-19 vaccine rollout
The specter of Manaus: the risks of a rapid return to pre-pandemic conditions after COVID-19 vaccine rollout Open
The development and deployment of several SARS-CoV-2 vaccines in a little over a year is an unprecedented achievement of modern medicine. The high levels of efficacy against transmission for some of these vaccines makes it feasible to use …
View article: Individually optimal choices can be collectively disastrous in COVID-19 disease control
Individually optimal choices can be collectively disastrous in COVID-19 disease control Open
Background The word ‘pandemic’ conjures dystopian images of bodies stacked in the streets and societies on the brink of collapse. Despite this frightening picture, denialism and noncompliance with public health measures are common in the h…
View article: Detecting in-school transmission of SARS-CoV-2 from case ratios and documented clusters
Detecting in-school transmission of SARS-CoV-2 from case ratios and documented clusters Open
Claims that in-person schooling has not amplified SARS-CoV-2 transmission are based on similar infection rates in schools and their surrounding communities and limited numbers of documented in-school transmission events. Simulations assumi…
View article: Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein
Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein Open
The spike protein receptor-binding domain (RBD) of SARS-CoV-2 is the molecular target for many vaccines and antibody-based prophylactics aimed at bringing COVID-19 under control. Such a narrow molecular focus raises the specter of viral im…