PCR

“Notable, Significant and Abnormal” Purchases of PCR Lab Equipment in Wuhan, Summer 2019

Researchers have uncovered “notable, significant and abnormal” purchases of PCR lab equipment in Wuhan in the summer of 2019, suggesting that Covid was spreading “virulently” in the city far earlier than was previously believed. The Telegraph has the story.

Analysts trawled through PCR procurement contracts in Hubei Province, of which Wuhan is the capital, and found spending had almost doubled on the previous year.

The study by Internet 2.0, a cyber security consultancy that specialises in examining data from China, says: “We have come to the conclusion that, based on the data analysed, it suggests the virus was highly likely to be spreading virulently in Wuhan, China, as early as the summer of 2019 and definitely by the autumn.”

The data and findings have been passed to U.S. Government officials amid growing speculation that the virus escaped from a lab in Wuhan and its existence was covered up for months.

According to the more accepted version of events, Covid originated in a “wet market” selling live animals in Wuhan at the beginning of December.

But the new report claims spending on PCR equipment – standard kit in laboratories for amplifying small amounts of DNA and critical in tracking Covid – in Hubei Province increased to £7.8 million in 2019 from £4 million the year before and £3.3 million in 2017.

The total 2019 contract value, according to Internet 2.0, was higher than the previous two years put together. The report also found the number of PCR contracts increased from 89 in 2018 to 135.

The report’s authors claim the growth in spending was accounted for by contracts at four main institutions – the Chinese Centres for Disease Control (CDC) in Hubei province, the Wuhan Institute of Virology, the Wuhan University of Science and Technology and a military hospital in Wuhan. The report says this is of huge importance because of the bodies’ roles in disease control and prevention.

The report alleges that the “significant increase in spending” was noticed from the summer of 2019, beginning as early as May – seven months before public health officials in China notified the World Health Organisation (WHO) that a mysterious illness was spreading through Wuhan.

The report concludes: “We assess with high confidence that the pandemic began much earlier than China informed the WHO about Covid.”

Worth reading in full.

ONS Admits Ignoring Manufacturer Instructions in PCR Testing

The Office for National Statistics has admitted that in its Covid infection survey it has been reporting PCR tests as positive when only a single coronavirus gene is detected, despite this being contrary to the instructions of the manufacturer that two or more target genes must be found before a positive result can be declared.

According to a rapid response in the BMJ this week by Dr Martin Neil, a statistics professor at the University of London, targeting only a single gene in this way massively increases the risk of a false positive because of the possibility of cross-reactivity with other coronaviruses as well as prevalent bacteria or other contamination.

Digging into the detail of the methods followed by the lighthouse laboratories which process the tests for the ONS, Professor Neil writes:

The kit used by the Glasgow and Milton Keynes lighthouse laboratories is the ThermoFisher TaqPath RT-PCR which tests for the presence of three target genes from SARS-COV-2. Despite Corman et al originating the use of PCR testing for SARS-CoV-2 genes there is no agreed international standard for SARS-COV-2 testing. Instead, the World Health Organisation (WHO) leaves it up to the manufacturer to determine what genes to use and instructs end users to adhere to the manufacturer instructions for use.

The WHO’s emergency use assessment for the ThermoFisher TaqPath kit includes the instruction manual and contained therein is an interpretation algorithm describing an unequivocal requirement that two or more target genes be detected before a positive result can be declared. The latest revision of ThermoFisher’s instruction manual contains the same algorithm. The WHO have been sufficiently concerned about correct use of RT-PCR kits that on January 20th 2021 they issued a notice for PCR users imploring them to review manufacturer instructions for use carefully and adhere to them fully.

The ONS’s report of December 5th 2020 lists SARS-CoV-2 positive results for valid two and three target gene combinations and the report of December 21st does the same, for samples processed by the Glasgow and Milton Keynes lighthouse laboratories. However, it also lists single gene detections as positive results.

Between a quarter and two thirds of positive results were affected, Professor Neil found.

Over the period reported the maximum weekly percentage of positives on a single gene is 38% for the whole of the UK for the week of February 1st. The overall UK average was 23%. The maximum percentage reported is 65%, in East England in the week beginning October 5th. In Wales it was 50%, in Northern Ireland it is 55% and in Scotland it was 56%. The full data including averages and maxima/minima are given in [17].

Although the non-compliant practice was clearly indicated in the ONS reports and confirmed in correspondence, it was denied by key figures when writing in the press.

Professor Alan McNally, Director of the University of Birmingham Turnkey laboratory, who helped set up the Milton Keynes lighthouse laboratory, contradicted what was stated in the ONS report in a Guardian newspaper article about the new variant. He reported that all lighthouse laboratories operated a policy that adhered to the manufacturer instructions for use: requiring two-or-more genes for positive detection.

In correspondence with Mr Nicholas Lewis about single gene testing, in February 2021, the ONS confirmed that they do indeed call single gene targets as positives in their COVID-19 Infection Survey and also confirmed that the samples are processed by UK lighthouse laboratories.

Is this one reason the ONS consistently reports higher Covid infections than the ZOE Covid Symptom Study, which tracks symptomatic Covid? In its latest report published today, the ONS estimates 192,300 people had Covid in the UK in the week ending March 13th, whereas ZOE estimates 109,400 people had symptomatic Covid in the middle of that week – almost half the number.

Two Thirds of Covid Cases in Schoolchildren Are False Positives Say Experts

Mass testing in schools as children returned this week is resulting in hundreds of positives – but viral prevalence is now so low that the large majority of them are wrong and result in children and their contacts isolating needlessly. Sarah Knapton in the Telegraph explains.

Biostaticians are concerned that infections in the community are now so low, that false positives and negatives are vastly outnumbering true cases, leading to real cases being missed and families needlessly being asked to isolate.

Pupils are currently being tested twice a week for coronavirus using lateral flow devices, but real-world data has shown they miss positive cases around 50% of the time.

Similarly, although they pick up 99.9% of negative cases, meaning fewer than 0.1% will be false positives, the prevalence rate is now low enough that false positives will be making a significant contribution to the overall figure.

Previously, positive tests were confirmed using a more accurate polymerase chain reaction (PCR) lab test, but this week the Government admitted it had quietly scrapped the process at the end of January.

It means that thousands of pupils and their families are having to isolate needlessly, and missing more school after months away from classrooms.

The latest figures from NHS Test and Trace in secondary schools found 328 positives out of 663,332 tests between February 25th and March 5th. That’s 1 in 2,000 pupils, which is far lower than the 1 in 270 that the latest ONS survey suggests is the current community prevalence. Some are concerned this means large numbers of cases are being missed, though the PCR-based ONS survey picks up many of the non-infectious cold positives which the less sensitive lateral flow tests (LFTs) do not. There is no reason to regard missing cold positives as a problem, particularly given the personal and economic cost of isolating positive cases.

In primary schools, 613 positives were found from 721,546 tests, or about 85 in 100,000. This gives an overall school prevalence rate of about 0.067%.

At this rate (if it were the true prevalence), out of a million tests 670 should come back as true positives. However, with a 0.1% false positive rate (a conservative estimate for LFTs, which were found in a report to have a 0.32% false positive rate) there would also be 1,000 false positives. That means 1,000 out of 1,670 positives, or around 60%, would be false. Of course, the 670 positives per million from the last couple of weeks of testing include the false positives, so the actual proportion of false positives will be higher.

Professor Jon Deeks, a biostatistician from the University of Birmingham, told the Telegraph:

We would expect far more false positives than true positives amongst those testing positives in schools. There are many uncertainties but given the DHSC data it seems likely that over 70% of positive test results are false positives, potentially many more. Addition of a confirmatory PCR would add little cost and would most likely reduce false positives to 1 in 1,000,000. The refusal to confirm lateral flow results with PCR is at best perplexing, will make testing less attractive, and create harm by wrongly isolating individuals, families and other close contacts.

Confirmatory PCR testing for LFT positives is unlikely to help, however, in terms of weeding out cold positives, as the PCR tests are much more sensitive than the LFTs (picking up many more cold positives) and so are unlikely to give a negative where an LFT has come out as a cold positive.

There is also the question of how many of the tests have been incorrectly carried out, perhaps on purpose, if self-administered, to avoid having to isolate?

Mass testing in schools was always a bad idea – cruel, intrusive, pointless. The high proportion of false positives, with their needless and disruptive requirement to self-isolate, only underlines that fact.