Diagnosis of SARS-CoV-2 - what are the options?
A summary of Kate Templeton's presentation at the SARS-CoV-2/COVID-19 workshop.
What we currently know about the disease course:
- Symptomless incubation period of an average of 5 days. At this point, the levels of virus may or may not be high enough to detect
- The first symptoms are usually a fever followed by a cough. At this point the viral load is much higher, usually peaking within a few days of the first symptoms
- An immune response should become detectable, but possibly not until around 14 days after infection
Because the immune response comes so much later in the disease course, an RT-PCR test to detect viral RNA is being used for rapid diagnosis. The RT-PCR test for SAR-CoV-2 targets the RdRP gene , and the average turnaround for NHS Lothian is around 12 hours from receipt of sample.
Challenges so far have included difficulties in obtaining consumables and swabs, and restrictions in which labs were able to work with the virus, which was classified as a Category 3 pathogen, though it has now been downgraded to Category 2. NHS Lothian aim to be able to test 700 per day, and up to 3,000 per day across all diagnostic labs in Scotland by the middle of April. Tests for NHS Lothian staff are already available.
Nose swabs appear to be better than throat swabs for mild virus detection, with higher viral loads, and samples from nose swabs giving positive qPCR responses for longer during the progression of the infection than throat swabs. At NHS Lothian, a combined nose and throat swab is being taken for the detection of mild infection. If the disease has progressed to pneumonia, only 60% of nose-throat swabs are still positive; in these cases, endotracheal secretions have so far remained 100% positive.
 Corman, V.M., et al., Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 2020. 25(3): p. 2000045.