Low Viral Diversity Limits the Effectiveness of Sequence-Based Transmission Inference for SARS-CoV-2-Reference-Cited by-同舟云学术

Low Viral Diversity Limits the Effectiveness of Sequence-Based Transmission Inference for SARS-CoV-2

Published:2023-02-21 Issue:1 Volume:8 Page:
ISSN:2379-5042
Container-title:mSphere
language:en
Short-container-title:mSphere

Author:

Farjo Mireille¹,Brooke Christopher B.¹²^ORCID

Affiliation:

1. Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA

2. Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA

Abstract

Tracking the spread of infection amongst individuals within and between communities has been a major challenge during viral outbreaks. With the unprecedented scale of viral sequence data collection during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, the possibility of using phylogenetics to reconstruct past transmission events has been explored as a more rigorous alternative to traditional contact tracing; however, the reliability of sequence-based inference of transmission networks has yet to be directly evaluated.

Funder

HHS | NIH | National Institute of Allergy and Infectious Diseases

Publisher

American Society for Microbiology

Subject

Molecular Biology,Microbiology

Link

https://journals.asm.org/doi/pdf/10.1128/msphere.00544-22

Reference20 articles.

1. Disease contact tracing in random and clustered networks

2. The Effectiveness of Contact Tracing in Emerging Epidemics

3. Bayesian Inference of Infectious Disease Transmission from Whole-Genome Sequence Data

4. Evolution of MRSA During Hospital Transmission and Intercontinental Spread

5. TNet: Phylogeny-Based Inference of Disease Transmission Networks Using Within-Host Strain Diversity