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Thu Mar 26, 2020, 07:05 PM

Chinese Retrospective Comparison Between RTPCR Covid Tests/Radiological Findings: False Negatives.

The paper I'll discuss in this post is this one: Correlation of Chest CT and RT-PCR Testing in Coronavirus Disease 2019 (COVID-19) in China: A Report of 1014 Cases

Earlier today, with reference to a post speculating on a shortage of instrumentation to conduct testing and lab staff, I remarked that I didn't think that was the case, based on general knowledge, since I assumed that the test was a PCR test and that there are a plethora of automated instruments that can do that. I stated that I believed the real issue with testing was more logistical and not related to equipment or even personnel at least to conduct the tests, since these devices are highly automated. (Interpretation is another matter, but even this can be streamlined with software.)

To confirm my suspicion, since I hadn't really looked at how the test works, I poked around briefly when I had a few spare minutes, something that doesn't happen that much while working from home.

The test according to the Chinese paper cited herein is in fact a PCR based test, which is not surprising, but if this paper is correct, the accuracy of the test is in question.

The normal regulatory pathway for a CLIA test - this is the class of tests that are approved for use in clinical settings - is actually quite rigorous in terms of acceptance. However nothing that went before is anything quite like Covid-19 and it is understandable that we go with what we can do rapidly based on an understanding of technology.

This paper however is a little disturbing. All the world's scientific publishers are working to make all Covid-19 related papers open sourced, so there is no need for me to discuss the details. The summary at the top of the paper is clear enough.

It reads:

Key Points
■ The positive rates of RT-PCR assay and chest CT imaging in our cohort were 59% (601/1014), and 88% (888/1014) for the diagnosis of suspected patients with COVID-19, respectively.

■ With RT-PCR as a reference, the sensitivity of chest CT imaging for COVID-19 was 97% (580/601). In patients with negative RT-PCR results but positive chest CT scans (n=308 patients), 48% (147/308) of patients were re-considered as highly likely cases, with 33% (103/308) as probable cases by a comprehensive evaluation.

■ With analysis of serial RT-PCR assays and CT scans, 60% to 93% of patients had initial positive chest CT consistent with COVID-19 before the initial positive RT-PCR results. 42% of patients showed improvement of follow-up chest CT scans before the RT-PCR results turning negative.

A brief excerpt from the introduction with some added bold on my part:

Since December 2019, a number of cases of “unknown viral pneumonia” related to a local Seafood Wholesale Market were reported in Wuhan City, Hubei Province, China (1). A novel coronavirus (SARS-CoV-2) was suspected to be the etiology with Phinolophus bat as the alleged origin (2). In just two months, the virus has spread from Wuhan to the whole China, and another 33 countries. By 24:00 on February 24, accumulative 77,658 confirmed cases with 9,126 severe cases and 2,663 deaths were documented in China (3), and 2,309 confirmed cased with 33 death were reported in other countries (including Japan, Korea, Italy, Singapore, Iran as the top five countries). As of 24:00 on February 11, a total of 1,716 confirmed cases and 1,303 clinically diagnosed cases of medical personnel were reported from 422 medical institutions, of which 5 died, accounting for 0.4% of the nationwide deaths during the same time period (4).

In absence of specific therapeutic drugs or vaccines for 2019 novel coronavirus disease (COVID-19), it is essential to detect the diseases at an early stage, and immediately isolate the infected person from the healthy population. According to the latest guideline of Diagnosis and Treatment of Pneumonitis Caused by 2019-nCoV (trial sixth version) published by the China government (5), the diagnosis of COVID-19 must be confirmed by the reverse transcription polymerase chain reaction (RT-PCR) or gene sequencing for respiratory or blood specimens, as the key indicator for hospitalization. However, with limitations of sample collection and transportation, and kit performance, the total positive rate of RT-PCR for throat swab samples was reported to be about 30% to 60% at initial presentation (6). In the current emergency, the low sensitivity of RT-PCR implies that many COVID-19 patients may not be identified...

I thought it worth pointing out.

I am very, very, very, very sure that scientists are working their collective asses off to improve this situation. We have some very dedicated and knowledgeable people working late into the night to address these concerns, to validate methods, to get the materials in place to handle them. (I know this from the emails I receive at work from biological suppliers.)

But this is worth considering and represents an important safety point. Just because a person has tested negative while sick does not absolutely imply that it is something other than Covid-19

Keep it in mind.

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Reply Chinese Retrospective Comparison Between RTPCR Covid Tests/Radiological Findings: False Negatives. (Original post)
NNadir Thursday OP
Turbineguy Thursday #1
cstanleytech Yesterday #2
NNadir Yesterday #3

Response to NNadir (Original post)

Thu Mar 26, 2020, 07:51 PM

1. This might explain

why so many get tested (presumably for the identified reasons) but only a few are positive. In Washington State 93% of tests come back negative.

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Response to Turbineguy (Reply #1)

Fri Mar 27, 2020, 02:26 AM

2. True but unless the error rate is high the odds are that most of the people are simply dealing with

something like a cold atleast for now.
Eventually of course as the infection rate climbs and assuming varies state and federal officials (mostly Republican and mostly interested in protecting themselves and Trump from this disaster they all helped create) keep their heads wedged up their butts and do not institute a nationwide quarantine for 4 weeks at a minimum soon the number will eventually surpass the number with the cold and or flu.

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Response to Turbineguy (Reply #1)

Fri Mar 27, 2020, 10:03 AM

3. The Chinese data doesn't show, however, a false positive rate as high as 93%.

It would not be surprising if some subset of the people tested using the same RT-PCR method would actually be infected.

Of course, we do not know if the tests used in Washington were better or worse than those used elsewhere.

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