Whole-genome sequencing – lessons for public health surveillance

Genomic sequencing has proven vital in detecting the source and variants of COVID-19, improving contact tracing, reducing disease transmission and ensuring health security for Australia. But genomic sequencing isn’t new and researchers from the NHMRC Centre of Digital Health (CRE) have been investigating it’s use in cases from public surveillance of Salmonella Typhimurium, predicting antibiotic

Byambasuren O, Dobler CC, Bell K, Rojas DP, Clark J, McLaws M-L, Glasziou P. Comparison of seroprevalence of SARS-CoV-2 infections with cumulative and imputed COVID-19 cases: systematic review. medRxiv. 2020:2020.07.13.20153163. preprint

Background. Accurate seroprevalence estimates of SARS-CoV-2 in different populations could clarify the extent to which current testing strategies are identifying all active infection, and hence the true magnitude and spread of the infection. Our primary objective was to identify valid seroprevalence studies of SARS-CoV-2 infection and compare their estimates with the reported and imputed COVID-19

Byambasuren O, Cardona M, Bell K, Clark J, McLaws M-L, Glasziou P. Estimating the extent of asymptomatic COVID-19 and its potential for community transmission: systematic review and meta-analysis. medRxiv. 2020:2020.05.10.20097543.

Background: The prevalence of true asymptomatic COVID-19 cases is critical to policy makers considering the effectiveness of mitigation measures against the SARS-CoV-2 pandemic. We aimed to synthesize all available research on the asymptomatic rates and transmission rates where possible. Methods: We searched PubMed, Embase, Cochrane COVID-19 trials, and Europe PMC (which covers pre-print platforms such

Rockett RJ, Arnott A, Lam C, Sadsad R, Timms V, Gray K-A, Eden J-S, Chang S, Gall M, Draper J, Sim EM, Bachmann NL, Carter I, Basile K, Byun R, O’Sullivan MV, Chen SCA, Maddocks S, Sorrell TC, Dwyer DE, Holmes EC, Kok J, Prokopenko M, Sintchenko V. Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modelling. Nature Medicine 2020; 26(9):1398-1404.

In January 2020, a novel betacoronavirus (family Coronaviridae), named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the etiological agent of a cluster of pneumonia cases occurring in Wuhan City, Hubei Province, China1,2. The disease arising from SARS-CoV-2 infection, coronavirus disease 2019 (COVID-19), subsequently spread rapidly causing a worldwide pandemic. Here we examine