COVID-19: Noguchi’s pool testing flawed – Bright Simons

Ghanaian social innovator, Bright Simons, has cited errors in the method used by the Noguchi Memorial Institute for Medical Research (NMIMR) in laboratory testing of coronavirus.

According to the Vice-President of the think-tank, IMANI, “only the mass screening exercises appear ethically suited for mass sampling. Routine surveillance and enhanced contact tracing cases, with their high pre-test positivity rates, on the other hand, are best not confirmed through pooled sampling”.

He was commenting on recent developments and questions raised about the over 100,000 tests conducted in Ghana so far.

The Head of Virology at Noguchi, Professor William Ampofo, had to clarify at a press briefing on Wednesday, April 22,  2020, that the research facility was using sample pooling to scale up the number of tests.

Critics have argued that the capacity of Noguchi did not support the daily results churned out.

“We simply pool the samples, meaning that, if you have 1,000 samples, you put them in groups of 10 and you test 100 pools at a time. So in a short time, instead of testing 1,000 samples, you actually test 10,000 samples. This method we are using now was derived in 1945, and this very efficient way we have proceeded,” Prof. Ampofo explained.

However, Mr Simons has questioned the method in comparison to other countries using similar procedures but higher standards.

Citing India, for example, Mr Simons explained that the Asian country was one of the few to commission an in-depth “efficacy and ethical review of whether to update the national protocol on testing by allowing pooled samples”.

India did so just a little over a week ago, but added many caveats, he observed and added that it should be of concern to Ghana too.

He explained that the Indian Council of Medical Research (ICMR) imposed a cap of five samples, a threshold Ghana initially adopted before “escalating” to 10 samples per well.

In his opinion, the method “speaks to the fear of overestimating diagnostic sensitivity thresholds”.

According to Mr Simons, India also permitted pooled sampling “only if the pre-test probability of positivity is lower than 2%”.

He indicated that Stanford’s Benjamin Pinsky, a clinical virologist, recently led a team to conduct mass community screening for Covid-19 (especially at sub-clinical level) in San Francisco.

Pinsky’s team determined that a pre-test probability of 1% is the reasonable threshold to allow pooled sampling, Mr Simons stressed.

“These precautions put in place in other epidemiological contexts raise important issues for Ghana’s continued use of pooled sampling.” He pointed out.

He observed that a pooled sampling protocol was highly responsive to the specifics of the test kit in use, the epidemiological background, and the goals of screening. Hence, protocols must be submitted for peer review and national-level ethical clearance, as has been done in India.

For him, the ethical issues were compounded because differential diagnosis remains the standard of care in a context like Covid-19, where observed symptoms could be highly non-specific.

“Many respiratory pathogens could be implicated in the clinical presentation. (Even some health workers have taken to calling SARS-COV-2, the microbe that causes Covid-19, a ‘flu virus’, but it belongs to a completely different family of viruses).

“In that regard, re-sampling for further tests could be warranted even if a negative result ensues. In a pooled testing scenario, this situation is complicated, especially in the absence of patient consent,” he explained.