Median and 90th Percentile Turnaround Time to Obtain Virus Whole Genome Sequencing Result From Time of COVID-19 Test

Name and Constituency of Member of Parliament
Dr Tan Wu Meng
MP for Jurong GRC

To ask the Minister for Health (a) what is the median and 90th percentile turnaround time to obtain a virus whole genome sequencing (WGS) result from the time a patient's COVID-19 test is reported as positive; (b) to date, how many COVID19 cases have case cluster linkages established through WGS assistance; and (c) how does this compare with the experience of other healthcare systems overseas.

Written Answer

The National Public Health Laboratory (NPHL) performs viral genomic sequencing for all confirmed COVID-19 cases. The average time taken to obtain a virus whole genome sequencing (WGS) result from the time a patient's COVID-19 test is reported as positive is seven days. The turnaround time of seven days is comparable to that of Australia and the United Kingdom (UK). A longer time may be taken for some specimens, such as if re-extraction is needed due to low viral load in the specimen.

Available WGS results are routinely used to discover or confirm linkages between cases and clusters, and to investigate possible transmission chains. From 26 October 2020 to 26 June 2021, 111 unlinked cases were subsequently linked after epidemiological investigations with the aid of WGS results.

All cluster investigations are supported by evidence from WGS and phylogenetic analysis when available. 70 Singapore is one of the few countries globally, including Australia, which uses WGS to trace and investigate transmission chains. Most countries, especially those with a high number of cases, do not use WGS for contact tracing but instead use it on a subset of cases to track the proportion of genotypes and variants. As such, it is difficult to make valid comparisons with other healthcare systems overseas.