Why are we seeing an increase in cases?

When we break a recent record for the number of COVID cases we have dramatic headlines.  On 7th Sept there were 2,048 new cases in the UK with 2,988 the day before up from around 1,500-1,900 in the preceding days.  This has created a spike over and above the already upward trend.  (I believe the upward trend that preceded it to be due to the increasing number of cases being tested as set out here). 

There are four possible explanations for the increase:

  1. There are now significant numbers of true positive cases appearing in addition to the background false positives.  The outbreaks in the North West are real and if they have taken another leap this will feed through to national data.
  2. The numbers being tested increased and the percentage testing positive remained similar.  These numbers are yet to be published for these two days.
  3. Testing laboratories had a bad couple of days with higher than usual false positive rates.
  4. When Pillar 3 or 4 antibody testing returns a positive result these values are added to the totals. It is not described whether this is done on a daily basis or in batches but this would artificially inflate the data.

The spike has been seen in England and the other nations, while showing an increase, appear to be following the general trend due to more testing. This supports the first hypothesis. If the rate of positivity in patients from the North West has reached 5% of those tested we would expect to see 2,800 cases a day assuming the rest of the country still had only false positives. That is one possible explanation for the rise. This would be a massive jump for that region and suggest the beginning of exponential growth.

Another explanation would be a spike in 20-29 year olds returning from holidays and this spike could be spread out more generally across the country.  However, without knowing the ages of those tested it is impossible to interpret the significance of a higher rate in any one age group.

Aside from these two sources of infection, there is another possible explanation.  Looking at data from testing since the end of June, when laboratories have had a higher false positive rate it tends to take a few days before it reverts to the mean.  A significant part of the uptick could be due to false positives.  This would be exacerbated if the number of tests carried out on 6th and 7th of September was record breaking. For example, if there were 200,000 tests with a false positive rate of 1.2% that would imply a rate in the North West of 2.5%.  If we either increased the testing to 250,000 tests or had a false positive rate at 1.4% then the spike is compatible with there being no excess of cases in the North West.

Even when the data showing the number of tests carried out is published, there will still be ambiguity over the contribution of the above factors to the rise. 

The numbers of false positive results are high and the daily fluctuations mean that on a national level it is worth being sceptical of spikes during the summer months.  Earlier in the summer there were similar fluctuations but the total numbers were smaller so the differences were less noticeable. Look out for the regional data to see genuine reasons for concern. When COVID returns it is likely to be regional to start with. 

Published by clarecraigfrcpath

I have been a pathologist since 2001 and a Consultant Pathologist since 2009. I worked for Imperial College Healthcare Trust as a cytopathologist until 2015. Subsequently I was the day to day Pathologist on the cancer arm of the 100,000 Genome Project and more recently I have worked for Panakeia, an AI digital pathology startup as Head of Pathology. I am currently between jobs and doing occasional consultancy work and crunching COVID data.

7 thoughts on “Why are we seeing an increase in cases?

  1. Would it not also increase the positive rate if more tests (as a percentage of total) were directed to known hotspots, for instance in the NW? Anecdotally, there has been reduced availability in non-hotspots, such as London.

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    1. Yes it would. However, focusing testing on areas where there is evidence of true positives would be a good way forward. Testing elsewhere should carry on to keep an eye out for new cases appearing but the results should be dismissed unless there is other evidence pointing to them being true positives e.g. serial positive PCR results, positive viral culture or ground glass findings on chest CT.

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  2. Are the daily positive cases being reported all true positive with supporting evidence or simply a pos PCR from one nasal swab? Also, is any discount given to the possibility of residual viral RNA fragments from a previous infection being the cause of the positive result rather than viable virus?

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    1. Current practice is to report a positive on the basis of a single PCR from one nasal swab. Guidance to change reporting criteria was issued on Monday. Some of the cases will have a repeat PCR of the same or a new swab before reporting. Much more needs to be done in my opinion.

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      1. To be fair, PCR is probably the most specific test in science. Problems only rear their head when you are mass testing a well population. For stopping epidemics it is fast and works well. Last problem lies with incomplete understanding of false positives. They are not just a lab error – they are also characteristics of the test population.

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  3. First of all, thanks for your blog and your invaluable work!

    It is clear that increasing the number of (PCR) tests increases the absolute number of positives (many false, some genuine). With more positives, more deaths (depending on “regulatory environment”) will be counted as “COVID-19 deaths”.

    What still puzzles me is that (referring to Germany here, official numbers from the Robert Koch Institute) starting from beginning of September the RATIO of positive tests increased a lot, from 0.8 % (roughly the false positive rate seen throughout the summer) to 9 % now.

    I have some qualitative explanations for this, but all are unconvincing for me:

    1. The PCR test picks up genetic fragments of the 4 other common Corona viruses (causing 30 % of the common cold). However, the false positives for this situation are reportedly only around 1 %, so this mechanism is clearly not strong enough.

    2. The cycle threshold was increased by/for the labs, resulting in more positive test results (most of them false). I cannot see any reason why this should be done.

    3. Quality of the lab testing has decreased sharply, resulting in decontamination and more positive tests. This feels unlikely, since the testing volume has not increased as sharply as the ratio of positive tests (1.1 million tests in week 34 versus 1.4 million tests in week 46).

    Thanks for any light you might be able to shed on this!

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