Herewith three items of pandemic news: the UK var­i­ant seems to spread faster in the young; what’s next in vaccines (by new contributor Doug Pardee); and the import of the PCR test cycle threshold. Plus the accustomed frippery.

It’s accepted that patients carrying a higher viral load of SARS-CoV-2 are more likely to experience a more severe course of Covid-19, and more likely to die of the disease. Writing in the NY Times, Apoorva Mandavilli links half a dozen papers (out of dozens that have appeared in recent months) attesting to this correlation.

It turns out that the most widely used test for the presence of a SARS-CoV-2 infection, the RT-PCR test (real-time polymerase chain reaction), has a feature that can give at least a rough estimate of viral load. This is the cycle threshold, or Ct value.

RT-PCR works by running multiple amplification steps to magnify RNA from the SARS-CoV-2 virus that may be present in a sample. The Ct value represents how many steps (doublings) are necessary before the test is able to detect any of the target RNA. Therefore the lower the Ct value in a positive test, the more virus was present to begin with; the higher the Ct, the less virus.

Most machines that process samples for RT-PCR tests are set to run between 35 to 40 cycles before reporting out a result, positive or negative, for the presence of SARS-CoV-2. As these tests were initially approved by the FDA, they were approved for “qualitative” use only: a yes-or-no answer to the question of whether any virus is present. While the machine may report out the Ct value at which virus was detected (not all such machines do), laboratories worked on the assumption that they were not allowed by the terms of the FDA authorization to give out this (quantitative) result.

Mandavilli reports that in December the FDA “said clinical labs might report not just whether a person was infected with the coronavirus, but an estimate of how much virus was carried in their body.” She does not give a link to any FDA material, and I have been unable to find any. Mandavilli also quotes two unnamed FDA sources who claimed that laboratories have been able all along to give out Ct values.

This would be news to most laboratories and also to most epidemiologists, some of whom have been pushing since the spring for labs to record Ct values.

When Dr. Anthony Fauci appeared as a guest on This Week in Virology last July (TWiV #641), he indicated that laboratories (mostly) were in possession of Ct values and would supply them if asked. It became a minor meme on TWiV in the following weeks: “Dr. Fauci can get the Ct value, but you can’t.”

Ct provides only a rough idea of viral load. Most experts agree that a positive RT-PCR test with a Ct of 35 or greater represents someone who is not transmitting the virus — what is being detected is not replication-competent virus, it is fragments of broken-down RNA. At such high Ct values, the sample may contain as few as hundreds of copies of RNA per milliliter. A Ct of 30 might indicate thousands of copies per ml; one in the low 20s, millions; one in the low teens, billions of copies per ml. Anyone with a Ct of 25 or below is likely to be infectious.

One reason why Ct is not an exact measure of viral load: samples might be collected just within the nasal cavity, or deep within (nasal-pharyngeal), or in the throat, or via saliva. The skill and experience of the person doing the collecting matter. All of these factors could result in differences of three or four orders of magnitude in the volume of viral RNA captured. That represents a difference of ten or more in the cycle threshold value, but biased in the pessimistic direction: whatever viral load the Ct value implies, there may be much more virus present, but there is probably not less.

Despite these limitations, knowing the Ct value associated with a test can provide useful information to the clinician. Mandavilli quotes Dr. Daniel Griffin (who will be familiar to regular readers) that tracking viral loads “can actually help us stratify risk,” for example in knowing which patients may need more frequent checks on their oxygen level.

Bottom line: before you get an RT-PCR test, try to find out whether the lab at which it will be processed knows the Ct value. If possible, prefer to get tested where the back-end lab knows this number. Ask for it alongside the yes-no result of your test.

The next vaccines
by Doug Pardee

A musing about vaccine futures…

No surprise to me, the word currently is that AstraZeneca’s AZD1222 Covid-19 vaccine candidate won’t be ready for early results readout and Emergency Use Authorization (EUA) in the US until April. As Keith has noted in an earlier posting, it’s already been authorized in the UK.

I wonder if it might not get a US EUA at all. The Phase 3 trials on that vaccine have been mishandled, and early data from non-US trials indicate a low efficacy compared with the two mRNA vaccines already authorized, at least when given in the dosage that the US trial is using. AstraZeneca isn’t a US company, and I’m thinking it’s possible that the FDA will reject the EUA request on “trial quality” and “risk/benefit (given available alter­na­tives)” grounds. A rejection could have a side benefit of showing the American public that the FDA isn’t granting EUAs willy-nilly.

Well before that time, we should be getting the early readout from the Janssen (Johnson & Johnson) single-dose vaccine candidate, JNJ-78436735. That’s expected to happen within the next few weeks. That vaccine uses the same technology as AstraZeneca’s: a non-replicating recombinant adenovirus vector. That means they took the spike protein RNA code from the SARS-CoV-2 virus and spliced it into the RNA for an adenovirus that’s been stripped of its ability to replicate. Once one of those modified viruses invades a host cell, it will produce the spike protein that triggers the immune system, but it’s unable to spread to other cells.

One technical difference: the spike protein in the J&J vaccine is the stabilized version created by the NIAID. That stabilized version is used by all of the leading candidates except AstraZeneca, who are using the spike protein from the initial Wuhan RNA report. Whether the stabilized version produces better immunity is an open question.

I’m very curious about the efficacy of the J&J vaccine, because they chose the AD26 human adenovirus as a base. About a decade back, surveys done for a potential Ebola vaccine showed relatively high rates of immunity to AD26 among people in the geographic areas of interest, but the US isn’t central Africa. It may not be a problem for the vaccine anyway: “Clinical trials have not revealed impact of pre-existing immunity to Ad26 on vaccine immunogenicity, even in the presence of Ad26 neutralizing antibody titers or Ad26-targeting T cell responses at baseline.”

J&J says they will sell their vaccine “at cost” until the pandemic is over. Since only one dose needs to be bought per person, it should be inexpensive. Low cost is another touted advantage of the AstraZeneca vaccine can­di­date (AZ has also pledged to distribute at cost in the Western world until mid-next year, and in the de­vel­oping world indefinitely). More recently J&J began a Phase III trial of JNJ-78436735 using a two-dose regimen; this probably won’t read out for several months at least.

A fifth candidate, Novavax’s NVX-CoV2373, has just started its US phase 3 trial. That one uses a different tech­nology than the others we’ve been hearing about. It’s a protein subunit with adjuvant. That vaccine tech­nology is now well established, having been used for vaccines against a variety of viral diseases including whooping cough, shingles, and HPV. That trial is going with a 2:1 vaccine:placebo ratio, with saline being used as the placebo. I personally wouldn’t expect an early readout on that one until maybe May.

Researchers out of University College London and other insti­tu­tions have produced a report (in preprint form) on their epi­demi­olog­ical and phylodynamic investigation of the spread of the UK variant of the coronavirus, SARS-CoV-2 lineage B.1.1.7, which they refer to as VOC (the virus of concern). One con­clu­sion that jumped out at me: they found a “small but sta­tis­tically significant shift towards under 20s being more affected by the VOC than non-VOC variants.” They are careful to clarify that the meaning of this statistical result is not clear.

The illustration (click for a larger version) is taken from Figure 4 in their paper. It indicates that in age groups 0-9 and 10-19, more new cases involve the VOC variant than the older variants. (There is a slight bump too in the 40-49 age group that may not be statistically significant.)

Two fripperies today. First up, a year on a northern Minnesota beaver dam.

Second, a contender for the most amazing juggling you have ever seen.