Evidence map›Paper›PMID 41106280›Full record

ReviewVirology2026

Quantitative viral dynamics: Methods for parameter estimation.

Angela Tower, Katherine Owens, Shadisadat Esmaeili, Joshua T Schiffer, Daniel B Reeves, Elissa J Schwartz

Abstract readReview
In one paragraph

Review in Virology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Angela TowerDepartment of Mathematics & Statistics, Washington State University, Pullman, WA, 99164, USA.
Katherine OwensVaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA.
Shadisadat EsmaeiliVaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA.
Joshua T SchifferDepartment of Mathematics & Statistics, Washington State University, Pullman, WA, 99164, USA; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA; Department of Medicine, University of Washington, Seattle, WA, 98109, USA.
Daniel B ReevesVaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA; Department of Global Health, University of Washington, Seattle, WA, 98109, USA.
Elissa J SchwartzDepartment of Mathematics & Statistics, Washington State University, Pullman, WA, 99164, USA; School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA. Electronic address: ejs@wsu.edu.

Funding

Characterizing determinants of primary KSHV infection among children and adolescents in UgandaR01CA239593 · NCI · FRED HUTCHINSON CANCER RESEARCH CENTER · PI OREM, JACKSON, PHIPPS, WARREN · 2019 to 2023
$2.9M
Phylodynamic mechanisms of HIV reservoir seeding and maintenanceR01AI186721 · NIAID · FRED HUTCHINSON CANCER CENTER · PI Daniel Reeves · 2024 to 2026
$2.6M
Mathematical modeling of optimal therapeutic combinations for HIV cureR01AI150500 · NIAID · FRED HUTCHINSON CANCER RESEARCH CENTER · PI SCHIFFER, JOSHUA TISDELL · 2020 to 2024
$2.3M
Early intervention with anti-proliferative therapy close to ART initiation to limit long-term SIV persistenceR01AI179457 · NIAID · FRED HUTCHINSON CANCER CENTER · PI Joseph Christopher Mudd, Joshua Tisdell Schiffer · 2024 to 2026
$2.3M
Simulating persistence and elimination of the HIV reservoirK25AI155224 · NIAID · FRED HUTCHINSON CANCER RESEARCH CENTER · PI REEVES, DANIEL · 2020 to 2024
$581k
NCI NIH HHS R01 CA239593NIAID NIH HHS K25 AI155224NIAID NIH HHS R01 AI150500NIAID NIH HHS R01 AI179457NIAID NIH HHS R01 AI186721
6 · The paper itself

Abstract

Fitting mathematical models of viral dynamics to serial, quantitative viral load data provides inferences on the mechanisms in virus infection. This process can reveal the speed and magnitude of viral replication, cell proliferation and death, immune responses, and/or treatment efficacy. Viral dynamics modeling involves developing conceptual models, translating them into equations, and applying the appropriate statistical tools to determine the optimal parameters such that the model recapitulates observations from human and animal infections. In this review, we outline the theoretical foundations needed to understand model fitting, parameter estimation, and what it means to achieve a good fit. We provide examples and explain the strengths and limitations of three commonly used model fitting approaches: individual fitting, population mixed effects fitting, and feature fitting. We briefly review fitting algorithms and highlight powerful available computer software packages that can be used for fitting and parameter estimation. We discuss different model types, parameter identifiability, and how future modeling efforts can leverage advances in multi-dimensional data. Finally, we conclude with simple guidelines for choosing the best approach based on available data and scientific questions.

Indexed as

Viral LoadVirus DiseasesVirusesAlgorithmsAnimalsHumansModels, BiologicalModels, TheoreticalSoftwareVirus ReplicationApproximate Bayesian computationData science softwareMarkov chain Monte CarloMathematical model fittingMaximum likelihoodNonlinear mixed effectsOrdinary differential equationsParameter estimationResidual sum of squaresStochastic approximation expectation maximizationViral dynamics

Identifiers

PMID41106280
PMCPMC13344342

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.