E-Poster Presentation Australian Society for Microbiology Annual Scientific Meeting 2021

Respiratory Viral Oligo Panel reveal the composition of virome in SARS-CoV-2 positive patients (#226)

Jessica Johnson-Mackinnon 1 2 , Jessica Agius 1 2 , Winkie Fong 1 2 , Connie Lam 1 , Rebecca Rockett 1 3 , Vitali Sintchenko 1 2 3
  1. Centre for Infectious Disease and Microbiology, Westmead, NSW, Australia
  2. University of Sydney, Sydney, NSW, Australia
  3. Marie Bashir Institute for Infectious Diseases and Biosecurity , University of Sydney, Sydney, NSW, Australia

Background: The role of respiratory virus co-infections in the clinical outcomes of SARS-CoV-2 disease remains controversial. Most reports examined a narrow spectrum of viruses due to over-reliance on targeted qRT-PCR assays. This study aims to (i) determine the sensitivity of the Illumina Respiratory Viral Oligo Panel (RVOP) to capture and sequence co-infections of human influenza A virus (HIA), respiratory syncytial virus (RSV) A, human adenovirus, and rhinovirus with SARS-CoV-2, and (ii) investigate respiratory viral infections over the course of mild (outpatients) and severe acute SARS-CoV-2 infection.

Methods: RVOP kit based on a capture-based methodology was used. It can simultaneously sequence the genomes of 43 distinct respiratory pathogens. Complete genomes of HIA, RSV A, human adenovirus, and rhinovirus were produced in order to determine the limit of detection. SARS-CoV-2 positive respiratory specimens were tested at low, medium and high concentrations for each pathogen (qPCR Cycle threshold (Ct) 18-25, Ct 25-30 and Ct 30-35, respectively) and simulated mixed viral respiratory infections. We also examined the virome of two cohorts of laboratory confirmed SARS-CoV-2 patients in New South Wales (NSW), Australia collected between March to September 2020. Longitudinal samples from patients admitted to hospital for SARS-CoV-2 (n = 8, average 4.6 swabs/participant) symptoms were analysed and compared with patients that presented with SARS-CoV-2 symptoms but were not admitted to hospital (n = 25, average 1.3 swabs SARS-CoV-2/participant).

Results: The RVOP was able to generate consensus genomes from simulated viral co-infections where each pathogen had a viral load of less than Ct30. 70 SARS-CoV-2 positive respiratory samples from 33 patients were examined. No viral co-infections were identified, however, 5 of the 8 inpatients showed co-infection with a variety of bacterial pathogens.

Discussion and Conclusions: These findings highlighted the high sensitivity and capacity of RVOP to identify respiratory virus and bacteria co-infections and can inform further improvement of routine public health genomic surveillance for other respiratory viruses and bacteria during and between epidemics.