Nucleic acid testing for SARS-CoV-2
The diagnostic test of choice for acute symptomatic COVID-19 disease is nucleic acid testing (NAT) performed on an appropriately collected upper or lower respiratory tract sample. NAT is performed using either in-house real-time polymerase chain reaction (RT-PCR) with SARS-CoV-2 specific probes, or commercial assays. In-house RT-PCR assays were used in the early stages of COVID-19 outbreak in Australia, but increasingly commercial assays have become available.
Commercial assays require laboratory evaluation before use in NSWHP. NAT assays incorporate one or two SARS-CoV-2 specific targets and may require confirmation in a reference laboratory. The in-laboratory turnaround time is about six hours, but more rapid NAT platforms are under necessary evaluation.
SARS-CoV-2 serology tests detect antibodies to SARS-CoV-2: these appear about 12 days after the onset of acute infection using immunofluorescence techniques, and include SARS-CoV-2 specific IgG, IgM and IgA.
Serology is generally not indicated in the diagnosis of acute symptomatic COVID-19 infection. Its main use is for the retrospective diagnosis of COVID-19 disease, or in sero-epidemiological studies to determine infection rates in the community. Ideally acute (at clinical presentation) and convalescent (three or more weeks after clinical presentation) serum collection is required for the retrospective diagnosis of COVID-19 disease.
Reliable automated SARS-CoV-2 serology tests are not yet in widespread use. Various rapid point-of-care finger prick assays for SARS-CoV-2 antibodies have been used, but their sensitivity and specificity remain uncertain. In general, they are less sensitive and specific than enzyme immunoassays, immunofluorescence or virus neutralisation.
The required sample is at least 8-10ml of blood collected in SST tube(s), requested for “Coronavirus serology”. Two samples at least 14 days apart (to demonstrate a fourfold rise in SARS-CoV-2 specific antibody titre) should be obtained.
The order should request “Coronavirus Serology”. Clinical information including date of illness onset, SARS- CoV-2 NAT result (if performed), travel history and reason for testing should be included with the request.
Prioritisation of testing
Sera from patients identified as requiring SARS-CoV-2 serologic testing by Health Protection NSW to inform their public health response will receive priority. Other samples will be stored for future testing. If the requesting clinician would like testing expedited, they should contact their local public health unit or the clinical microbiologist at NSWHP, ICPMR – Westmead.
Interpretation of results
Data so far suggests that the antibodies may be detected from day 12 after illness onset. A fourfold rise in SARS-CoV-2 antibodies between acute and convalescent sera collection is diagnostic of recent infection.
SARS-CoV-2 isolation is performed in a Biological Safety Laboratory Level 3 (BSL-3) facility, and generally takes four to five days. It is not done in routine clinical practice as it is less sensitive and slower than NAT. It may have a role in determining infectivity, and provides material for NAT and serology assays.
Whole Genome Sequencing
Whole Genome Sequencing (WGS) can be performed on clinical samples or viral isolates. It can be used to confirm NAT results, but it is usually used to investigate transmission patterns of SARS-CoV-2 in conjunction with public health authorities.