Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults

This observational study was designed to determine the cellular tropism of Influenza A and B Viruses (IAV, IBV) from samples taken from the upper respiratory tract collected during routine nasal washes during the 2017-2018 season. Using single-cell RNA sequencing (scRNA-seq) we sought to determine which cell types could be infected, what the cellular response was to infection in both infected and bystander cells, and to compare the intra/inter-host variability of IAV and IBV during a single season at a single healthcare provider location.

• Study Design:
  • Prospective Longitudinal Cohort
• Study Type:
  • Cohort
• Total number of consented subjects: 18
• Subject Sample Telemetry Report (SSTR)

• BioProject
• PubMed
• Sequence Read Archive
• MeSH
• PMC

ADMITTED PATIENTS - CASES

Admitted Patients Inclusion Criteria:

To be included in the study, subjects must be

1. Over 18 years of age
2. Able to review and sign the Informed Consent Form
3. Able to review and sign the "Authorization to disclose protected health information for research purposes" form
4. Test positive for influenza A or B virus or RSV by Rapid Antigen Test (RAT) of the nasopharynx or by polymerase chain reaction (PCR) test in the previous 24 hours to 7 days
5. English-speaking subjects only

Admitted Patients Exclusion Criteria:

Potential subjects will be excluded by the following criteria:

1. Have a hematocrit less than 20 mg/dL
2. Are pregnant
3. Are under the age of 18 years
4. Are prisoners/vulnerable populations
5. Are employees of the PI or Co-I
6. Cognitively impaired adults

HEALTHY CONTROL SUBJECTS

Inclusion Criteria:

To be included in the study, subjects must be:

1. Over 18 years of age
2. Able to review and sign the Informed Consent Form
3. Able to review and sign the "Authorization to disclose protected health information for research purposes" form
4. English-speaking subjects only

Exclusion Criteria:

Potential subjects will be excluded by the following criteria:

1. Have a hematocrit less than 20 mg/dL
2. Are pregnant
3. Are under the age of 18 years
4. Are prisoners/vulnerable populations
5. Are employees of the PI or Co-I
6. Cognitively impaired adults

• Primary Phenotype: Influenza, Human

• Principal Investigator
  • Robert W. Finberg, MD. University of Massachusetts Medical School, Worcester, MA, USA.
• Co-Investigator
  • Manuel Garber, PhD. University of Massachusetts Medical School, Worcester, MA, USA.
  • Jennifer P. Wang, MD. University of Massachusetts Medical School, Worcester, MA, USA.
• Funding Source
  • Peer Reviewed Medical Research Program: Focused Program Award - Award Number: W81XWH-15-1-0317. Department of Defense - Congressionally Directed Medical Research Programs, Fort Detrick, MD, USA.