Should all the covid patients be isolated? Are they all infectious? No. Only those with sufficient viral loads would infect. If so, why not judiciously detect the high viral load patients?
There is a growing concern among the epidemiologists that the widely used, RT-PCR, a gold standard test, is so sensitive that it is not that useful in the present phase of pandemic. In RT-PCR, the number of amplification cycles needed to find the virus, called the cycle threshold, Ct, is set in most of the machines by the manufacturers at 40, a few at 37. This sensitivity is set from the point of view of not to miss the RNA at ‘any cost’.
Would this high sensitivity be counter productive now?
A major drawback of PCR and other diagnostic approaches (including RAT) is that they all fail to determine virus infectivity; PCR sensitivity is excellent but specificity for detecting replicative virus is poor. A typical study (3), involving symptomatic individuals, utilising a cross-sectional approach to correlate COVID-19 symptom onset to specimen collection with SARS-CoV-2 E gene RT-PCR and virus viability as determined by cell culture was conducted. These results demonstrate that infectivity (as defined by growth in cell culture) is significantly reduced when RT-PCR Ct values are > 24. For every 1-unit increase in Ct, the odds ratio for infectivity decreased by 32%. The high specificity of Ct and STT (Symptoms To Test) suggests that Ct values > 24, along with duration of symptoms > 8 days, may be used in combination to determine duration of infectivity in patients.

In another study (2) of three sets of testing data that include cycle thresholds, compiled by officials in Massachusetts, New York and Nevada, it was found that up to 90 percent of people testing positive carried barely any virus. They had Ct values set between 37-40.
Any test with a cycle threshold above 35 is too sensitive. Tests with thresholds so high may detect not just live virus but also genetic fragments, leftovers from infection that pose no particular risk — akin to finding a hair in a room long after a person has left.
People infected with the virus are most infectious from a day or two to about five to eight days after getting infected irrespective of appearance of symptoms. But with a low Ct threshold, the start phase might give a negative result. But in a few days, the viral load would increase sufficient enough to get a ‘positive’ and again it will taper out to give a ‘negative’. Only a delayed, repeat test (with a gap of 4 or 5 days) could confirm the phase! But at the current testing rates, it is impossible to do frequent testing to capture somebody in that window. It is more so if the person is asymptomatic with potential viral loads. Repeat tests, while only some can afford, may be a heavy burden on the health infra if adopted as a policy by the state.
From these analysis, there appears a strong case for lowering the threshold which is set very conservatively in India at 40. But, it is discounted by many, including the ICMR. Why ICMR is not inclined to take these suggestions and update their advisories, which are now followed in the west? The concern is from the fact that the amount of viral loads collected in swabs is not quantitative. Hence detection could differ even with same Ct values? Hence it would not give a reliable guidance. But, a conservative cutoff could be 30 to 35, may be at 30 could be a solution.
Alternatively, if Ct in RT-PCR could not give a dependable conclusion, then why not adopt RAT, that would only qualitatively give positives based on the ‘infectability’. The usual blame of ‘false negatives‘ that is missing out some positives (5%) may be due to low viral loads.
The latest protocol and advisory of ICMR on this strategy encompasses most of the concerns. It is now for the implementing states to follow. Higher dependence on RT-PCR by some states could delay the end of the ‘war’.
There is yet another dimension to the high sensitivity of RT-PCR: one may not get a negative test after the standard two weeks isolation. Only an anti body test could confirm the absence of infection. In some states, negative tests are demanded for removing the quarantine requirement. RT-PCR may be a gold standard since it detects even a fragment of dead virus! But would it not mislead the less informed health authorities?This could also be a reason for ‘alarming‘ reports of ‘reinfection‘!
Presently, the strategy of isolation of the infected is until 2 negative NP RT-PCR results 48 hours apart after 14 days of symptoms. Since, RT-PCR positivity persists significantly beyond infectivity is It is appropriate to adopt the Clinical criteria of 14 days from symptom onset or 72 hours symptom free (whichever is longer), to avoid any unnecessary isolation, and use of personal protective equipment and testing resources. And avoidable restrictions to the infected and their near and dear.
For asymptomatics, a 14 day quarantine without retesting would be sufficient.
The RT PCR with the present protocols would not at all miss a positive case but, some ‘false positives‘ can’t be ruled out. On the other hand, why not accept certain missed cases with Rapid Antigen Test that gives some ‘false negatives‘. If RAT is adopted to test only for asymptomatics, the error would not be damaging from infection control point of view: The missed cases would not spread the infection as RAT misses them only due to low viral loads. The error is manageable and acceptable in such demographically large and economically challenging country like India.
But, for heaven’s sake let us not report unnecessarily high case numbers with very sensitive RT-PCR, and frighten the general public.
Credits:
2. https://www.nytimes.com/2020/08/29/health/coronavirus-testing.html?referringSource=articleShare
3. https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciaa638/5842165

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