Lowest Positivity since July? Yes, but…

Headlines this morning proclaimed that Israel recorded the lowest coronavirus test positivity since July. Yesterday, just 5.4% of PCR tests for RNA from the SARS-CoV-2 virus found what they were looking for, the lowest percentage since early July.

Let’s look at that number a bit deeper.

Israel’s testing regimen

Israel has fairly high per-capita testing for the coronavirus. In September, 1.25 million tests were administered, enough for 14% of the whole population.

Israel tests three categories of people for the virus:

  1. Suspected cases: people who’ve either been exposed to a Covid-19 case or who have symptoms of the disease.
  2. Surveillance: The “Magen Avot” testing programme tests the residents of care homes regularly to identify outbreaks early. Also in this category is testing before scheduled medical procedures, testing before overseas travel, tests demanded by employers before returning to work, tests of yeshiva ‘capsules’ and any other kind of testing of people who aren’t suspected of having the virus.
  3. Recovery: some confirmed Covid-19 cases, usually those in the hospital, are tested to see if they are still positive. In some cases, a patient might have a few of these tests until eventually testing negative.

When Israel reports its daily ‘positivity’ number, it is calculated from the total number of new cases discovered divided by the total number of tests to identify new cases (categories 1 and 2 together).

This has some odd impacts on the numbers. It means positivity goes down when the airports are open, because more Israelis are getting pre-flight tests that many countries and airlines demand. It means when case numbers are high, positivity rises disproportionately because the surveillance programmes are scaled back to make more testing capacity available.

Better, but worse than July

Yesterday, Israel processed 44,465 tests, of which 2,837 were in category three. 2,264 of the remaining 41,628 were positive, which works out to a positivity of 5.44%.

The last time Israel had a day where less than 5.44% of tests came back positive was the 9th of July, more than three months ago. But that doesn’t mean things are better now than they have been since July, for a few reasons.

First, back on the 9th of July, 1,322 cases were found in 28,162 tests (5.35% positivity). Yesterday, 2,264 cases were found. If they’d done 44,500 tests in July like they did today, it’s highly likely that they’d have found more cases, but would also have tested a lot more healthy people, reducing the overall positivity.

Secondly, the incidence of coronavirus infections is a lot higher than it was back in early July. On 9 June, Israel reported 15,000 cases; today Israel reports 45,000 cases. But that’s actually a bit misleading. In July, to be removed as an active case required a negative test, which can take several weeks. Now, cases are automatically considered ‘recovered’ 10 days from the start of symptoms.

The hospitals haven’t recovered either. On the 9th of July, 87 Israelis were considered serious Covid-19 cases, of which 41 Israelis were on ventilators. Today, 244 are on ventilators out of 780 serious cases. Those numbers won’t drop quickly, as a small but increasing number of serious cases are hospitalised for months.

Number of Covid-19 patients on ventilators in Israel

More “past positives” could inflate positivity

One last confounding factor to consider. The false positive rate of the PCR test for coronavirus RNA is very low. We know this because in May, Israel was carrying out 5000 tests a day but only finding a few dozen cases. If you tested positive, you probably were infected with the coronavirus.

But “you were infected” isn’t the same as “you ARE infected”. The PCR test detects, essentially, bits of the virus. It doesn’t know if those bits are parts of functioning viruses that can infect cells and replicate, or if they’re the broken parts of inactive viruses smashed by the immune system.

So it’s possible to test positive for the coronavirus even if you’ve already beaten it. After the peak of infections, more of the people who test positive for the first time will have already beaten the virus and won’t be infectious. But they’ll still boost the positivity rate for a couple of weeks.

Reopenings have already started, with some yeshivot already back and most returning on Sunday. Kindergartens and workplaces are likely to reopen next week, too. These next few days are critical to lower virus incidence, keep R low (experts estimate R is around 0.7), and allow the country to slowly increase its R spending while keeping the virus under control.