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

High rates of within-host variability of SARS-CoV-2 in hospitalised patients (#338)

Jessica Agius 1 2 , Jessica Johnson-Mackinnon 1 2 , Winkie Fong 1 2 , Connie Lam 2 , Rebecca Rockett 2 3 , Vitali Sintchenko 1 2 3
  1. Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
  2. Institute for Clinical Pathology and Medical Research , Centre for Infectious Diseases and Microbiology Public Health, Westmead, NSW, Australia
  3. Marie Bashir Institute for Infectious Diseases and Biosecurity, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia

Background: Detection and understanding of low frequency variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) within hosts is becoming increasingly important. These variants provide early indications of potential diagnostic PCR dropouts, and can inform public health surveillance and tracking of cases. In addition, detecting low frequency variants may predict the positive selection of functional mutations, particularly as growing numbers of SARS-CoV-2 variants of interest and concern emerge. This study aims to investigate and quantify within-host variability over the course of mild (outpatients) and severe (inpatient) SARS-CoV-2 infection.  

Methods: The SARS-CoV-2 genomic diversity was examined in two cohorts of SARS-CoV-2 positive patients in New South Wales, Australia collected between March to September 2020. Longitudinal samples from patients admitted to hospital for SARS-CoV-2 (n = 8, average 4.6 swabs per participant) were analysed and compared with patients that presented with SARS-CoV-2 symptoms but were not admitted (n = 25, average 1.3 swabs SARS-CoV-2/ participant). The genomes were sequenced using Nextera protocol (Illumina). We utilised Illumina’s Respiratory Viral Oligo Panel (RVOP) which has been shown to generate more even genome coverage, has fewer amplification dropouts, and a higher sensitivity to detect low frequency variants.

Results: Seventy SARS-CoV-2 consensus genomes were recovered from 33 patients. Overall, low frequency variants were detected in 44% (11/25) of the cohort of patients with severe infection and 75% (6/8) of the admitted cohort. This included within-host variation seen at SNP sites across multiple samples taken during the patient’s hospitalisation.

Discussion and Conclusions: Our findings demonstrated the ability of probe-based capture methods to produce consistent SARS-CoV-2 genome coverage with the resolution sufficient to detect changes in the within-host low frequency variant populations. This method may help predict variant sites under selective pressure. Monitoring these variants is critical to ensuring ongoing effectiveness of immunisation and will assist in the design of future vaccines and therapeutics.