How testing can clear Covid-19 cases – Expert Reaction

Grey area in the test results of recent community Covid-19 cases has left health authorities conducting follow-up tests for more clarity.

Dr Ashley Bloomfield said yesterday it’s “too early to make a firm conclusion” around whether the two Auckland cases are current infections. Genome sequencing today showed they had the South African variant and that they were linked to the same source case in managed isolation as the Northland woman who tested positive on Sunday after leaving managed isolation. Health officials are now awaiting serology test results tomorrow.

The SMC previously asked experts to comment on serology testing, and how New Zealand could improve its Covid-19 testing strategy. The Ministry of Health also has a rundown of the types of Covid-19 tests.

The SMC asked experts to comment on what current Covid tests can and can’t tell us.

Dr Nikki Moreland, Senior Lecturer in Immunology, University of Auckland, comments:

“Serology testing measures antibodies that the body makes in response to infection. It generally takes 10-14 days after an initial exposure to SARS-CoV-2 before someone has a level of antibodies that would measure as positive on a serology test.

“That means if someone was infected in the last few days they are less likely to be positive by serology. So serology testing could provide another piece in the puzzle in determining the infection timeframe on these cases.”

No conflict of interest declared.

Associate Professor James Ussher, Department of Microbiology and Immunology, University of Otago, comments:

“​PCR tests detect the presence of viral genes in the sample (the gene targeted varies by assay). Importantly, PCR cannot determine whether or not infectious virus is present or if the patient is infectious. Previous studies have suggested that infectious virus is more likely to be cultured in samples strongly positive by PCR, virus can still be cultured from some samples that are weakly positive by PCR, and virus culture is only a proxy measure of infectivity (and probably lacks accuracy). Timing of sample collection relative is also important, as virus can rarely be cultured from late in the second week of illness, regardless of how strongly positive the PCR is.

“We can get an idea of how much virus is present in the sample by looking at the Ct (cycle threshold) value: the lower the Ct the more copies of the virus are present.

“In the first few days after infection the PCR will be negative. Once virus becomes detectable the amount will rapidly increase (lower Ct value) and before decreasing over the next few days to weeks (higher Ct value). There can be a long tail of PCR positivity at low levels (high Ct value) that can last for several weeks or even months; in some patients, tests may be intermittently positive at low levels and negative. A sample with a high Ct value (weak positive) may be due to early infection (in which case the PCR should become more strongly positive on repeat testing), due to past infection (anything from days to months), a sampling issue, or due to low level infection.

“It is not possible to accurately time the infection or determine infectivity with the PCR test. The test needs to be taken in context of the patient’s symptoms, exposure history, and previous test results. In the latest Covid cases in New Zealand, the two previous negative test results would suggest infection was recently acquired; the high Ct result could be due to early detection, testing during the recovery phase, or due to suboptimal sampling. Combined with the results of sequencing of the virus, it would seem most likely that this is recent acquisition in the managed quarantine facility.

“​If tested soon after exposure, then an infected contact may be falsely negative. Close contacts need to remain in isolation and be retested as per Public Health guidance. Casual contacts should be retested if they develop symptoms. Anyone in the population who develops symptoms that are consistent with COVID-19 (see the Ministry of Health’s case definition) should get tested. It is only by maintaining a high level of community surveillance that we will be able to rapidly detect community transmission. Along with scanning of QR codes and enabling Bluetooth contact tracing, this is the most important thing that New Zealanders can do to control the spread of the SARS-CoV-2 virus in the community should it be introduced across the border.”

No conflict of interest declared.

John Mackay, Technical Director at dnature diagnostics & research Ltd, comments:

“It is difficult to establish the infectiousness of a person based on a low viral load (the “high CT (cycle threshold)” spoken of). Indeed, a new preprint (not peer reviewed) suggests that detection of viral RNA via the commonly-used nasopharyngeal sampling swabs persists for many weeks post-infection, as compared with samples such as saliva.

“Positive Covid tests are confirmed using additional tests that target other regions of the viral genome – to ensure a true positive detection.

“Samples with low viral loads are also difficult as there may be insufficient RNA available from the sample to perform the genome sequencing of the virus. While many internationally disregard such samples as ‘false positives’, in a country such as NZ where the prevalence is very low, the combined detection and strain identification via genome sequencing or new qPCR tests specific for the variants of concern, provide crucial information on helping link cases and track possible routes of infection.

No conflict of interest declared.