Journal Article

Virome Data Explorer: A web resource to longitudinally explore respiratory viral infections, their interactions with other pathogens and host transcriptomic changes in over 100 people

Filip, Ioan, Youssef, Mariam, Morita, Haruka, Galanti, Marta, Lane, Benjamin, Patiño-Galindo, Juan Angel, Natesan, Sanjay, Ligon, Chanel, Comito, Devon, Elliott, Oliver, Perea-Chamblee, Tomin, Shaman, Jeffrey, Ibrahim, Sadiat, Shittu, Atinuke, Galianese, Angelica, Tagne, Eudosie, Rosenbloom, Daniel Scholes, Matienzo, Nelsa, Rabadan, Raul

2024

Overview

Viral respiratory infections are an important public health concern due to their prevalence, transmissibility, and potential to cause serious disease. Disease severity is the product of several factors beyond the presence of the infectious agent, including specific host immune responses, host genetic makeup, and bacterial coinfections. To understand these interactions within natural infections, we designed a longitudinal cohort study actively surveilling respiratory viruses over the course of 19 months (2016 to 2018) in a diverse cohort in New York City. We integrated the molecular characterization of 800+ nasopharyngeal samples with clinical data from 104 participants. Transcriptomic data enabled the identification of respiratory pathogens in nasopharyngeal samples, the characterization of markers of immune response, the identification of signatures associated with symptom severity, individual viruses, and bacterial coinfections. Specific results include a rapid restoration of baseline conditions after infection, significant transcriptomic differences between symptomatic and asymptomatic infections, and qualitatively similar responses across different viruses. We created an interactive computational resource (Virome Data Explorer) to facilitate access to the data and visualization of analytical results.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Adenoviruses / Adenoviruses, Human / Analysis / Asymptomatic / Bacteria / Biology and Life Sciences / Computer simulation / Computer-generated environments / Coronaviruses / Datasets / Disease / Enrollments / Gene expression / Genetic aspects / Identification and classification / Immune response / Immune system / Infections / Influenza / Internet resources / Medicine and Health Sciences / Methods / Methods and Resources / Pathogenic microorganisms / Pathogens / Public health / Respiratory diseases / Respiratory syncytial virus / Respiratory tract infection / Transcriptomics / Viral infections / Viruses