Print  Close

Accounting for reporting delays in real-time phylodynamic analyses with preferential sampling

Abstract Number:

2293 

Submission Type:

Contributed Abstract 

Contributed Abstract Type:

Speed 

Participants:

Catalina Medina (1), Julia Palacios (2), Lorenzo Cappello (3), Volodymyr Minin (4)

Institutions:

(1) University of California, Irvine, N/A, (2) Stanford University, N/A, (3) Pompeu Fabra University, Spain, (4) University of California-Irvine, N/A

Co-Author(s):

Julia Palacios  
Stanford University
Lorenzo Cappello  
Pompeu Fabra University
Volodymyr Minin  
University of California-Irvine

First Author:

Catalina Medina  
University of California, Irvine

Presenting Author:

Catalina Medina  
University of California, Irvine

Abstract Text:

The ongoing pandemic demonstrated that fast and accurate analysis of continually collected infectious disease surveillance data is crucial for situational awareness and policy making. Phylodynamic analysis uses genetic sequences of a pathogen to estimate changes in its genetic diversity in a population of interest, the effective population size, which under certain conditions can be connected to the number of infections in the population. Phylodynamics is an important tool because its methods utilize a data source in a way that is resilient to the ascertainment biases present in traditional surveillance data. Unfortunately, it takes weeks or months to sequence and obtain the sampled pathogen genome for use in such analyses. When the number of infections depends on the sampling frequency, the missing data results in underestimation of the effective population size. Here we present a method that affords reliable estimation of the effective population size trajectory closer to the time of data collection, allowing for policy decisions to be based on more recent data, with a better understanding of the limitations and uncertainties of such inference.

Keywords:

infectious disease dynamics|disease surveillance|Bayesian phylogenetics|genomic epidemiology|Bayesian nonparametrics|

Sponsors:

Section on Bayesian Statistical Science

Tracks:

Applications in Life Sciences and Medicine

Can this be considered for alternate subtype?

Yes

Are you interested in volunteering to serve as a session chair?

No

I have read and understand that JSM participants must abide by the Participant Guidelines.

Yes

I understand that JSM participants must register and pay the appropriate registration fee by June 1, 2024. The registration fee is non-refundable.

I understand