Saturday, February 22, 2020

Coronavirus from a laboratory quality perspective.

Call me paranoid or jaded, but I have become increasingly uncomfortable with the news about the current coronavirus outbreak.  

Over the weeks that all this has been going on what we have been told in the public media is that this is a new virus.  This is possible, but maybe not.  What is probably closer to the truth is that this is the first time it has come to light with the availabilities of today’s science technologies.  

Coronaviruses are ubiquitous, and while hardly ever tested, they and rhinoviruses probably are responsible for the vast majority of  common cold that circulate around the world all the time.  Some are found in non-human mammals (civet cats, camels, bats, pangolins), but many reside in humans and cause what is usually thought of a benign illness.

Note: while we all understand colds are a benign nuisance  in healthy children and adults, common colds are a significant cause of death in the very elderly (Hung IFN et al, Unexpectedly Higher Morbidity and Mortality of Hospitalized Elderly Patients Associated with Rhinovirus Compared with Influenza Virus Respiratory Tract Infection.  Int J Mol Sci. 2017 Feb; 18(2): 259. ), at a rate significantly higher than influenza or covid-19.

A new nucleic acid test was developed very quickly to help identify the presence of this new virus in people’s noses and respiratory secretions.  It was based on the nucleic acids of one of the first isolates found in China.  The test used is said to be  very specific, but I suspect that it was NOT tested for reactivity with other coronaviruses normally found in humans.  (Maybe I’m wrong on this but few virus banks would have enough common cold viruses available in their freezers.
The test that was developed was created in a highly specialized laboratories under very controlled ideal conditions.  There are very specific requirements for how the sample should be collected and how the sample to be kept cold (between 2-8oC) and be transported on ice.  If routine laboratory testing is taken as an indicator of how often that happens, we can say with almost certainty, many do not get that treatment.
Most people who are tested are either totally symptom free or have a mild cold.  That would be typical of about 80 percent of people living in the northern hemisphere in January and February.  That appears to be true for people who test positive and who test negative.  The vast majority remain that way from the beginning of their inspection to the end.  

If you go into a typical busy laboratory in North America the number of tests that get incorrectly labelled is very low, and often when incorrect labelling does occur it is usually with either infants or adults with communication problems (poor hearing or distraction or communication in a language other than what the laboratory workers communicate in).   Usually busy laboratories have a semblance of organization.  I suspect that when samples are collected by people working under stress, wearing hazmat suits and dealing with hundreds of stressed people, the rate of incorrect labelling goes up significantly. 

So just because the label says the sample came from John Smith, maybe it actually came from Joe Smith, or John Smithe, or Jane Smith, or maybe the guy who was in line but just after John Smith.

When these tests were designed it was in a controlled laboratory with research organized staff.  In the real world laboratory where there are hundreds or thousands of samples, the opportunity for error or confusion while testing mounts considerably. 
Finally, when tests are done in routine laboratories there are all sorts of Quality Control checks to make sure that the tests are working correctly.  

So in summary, this is a new test being used to test people who have no symptoms or any way to correlate with results.  The samples are being collected in chaotic situations with high stress.  And there is no other confirming test available. 
So with the highest regard for my laboratory colleagues, I suspect that the risks of errors going by undetected is considerable.  

Bottom line: 
Be VERY careful when you listen, watch or read in the media about what is going on.  The opportunity for the information to be at best misleading and at worse wrong is probably substantial.


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