December 22, 2020

expert reaction to PHE’s technical briefing document on the novel SARS-COV-2 variant, published on Monday 21 December 2020

A technical briefing document on the SARS-CoV-2 variant of concern, VUI-202012/01, was published yesterday by Public Health England (PHE).

Prof Sheila Bird, Formerly Programme Leader, MRC Biostatistics Unit, University of Cambridge, said:

“Over the weekend, I could not make numerical sense of the data on the new vARS-CoV-2 Variant of Concern (VOC) as reported at No10 Pres Conference and by the UK’s Genomic Consortium because swab-dates were not specified; nor was there information on the proportion of swabs sent for genomic analysis from the regions of England which are now designated as Tier 4.  Thankfully, the PHE report provides some of the missing answers.

“For example, percentage of SARS-CoV-2 positive swabs sent from Kent for genomic analysis was 4% (255/6130).

“The new variant of concern seems to have been identified due to a large phylogenetic cluster of 117 genomically similar cases in Kent during the week of 10-18 November.  This seems not to have been an outbreak investigation;  just routine samples.

“Thereafter, the variant was tracked back through the national phylogeny which showed that the Kent cluster of 117 was part of a larger cluster of 962.  Swab-date is available for 915/962, as shown in Table.

“PHE has noted that 97% of [HOW MANY?] Pillar 2 PCR tests which test negative on the S-gene target and positive on other targets are due to VOC.  Of course, we also need to know what percentage of 915 recent VOC positives tested negative on the S-gene target and positive on other targets.

“Increasing the sampling fraction for genomic analysis may not be an option if capacity is limited.  Hence, PHE proposed instead to use the frequency of S-gene target negatives among Pillar 2 PCR positives as a proxy for the frequency of VOC – but recognised limitations historically due to older virus variants which also test negative on spike.  Even limited genome capacity could perhaps tolerate some capacity being used to good effect to sort out genuine VOCs from proxy-contenders.

“Meanwhile, PHE’s proxy allowed comparison between recent-past growth-rate in S-negative versus S-positive cases which is how PHE has concluded that the relative transmission-fitness for VOC is 1.5 (95% CI: 1.34 to 1.59).  See PHE’s supporting figure [p10].”

‘Investigation of novel SARS-COV-2 variant: Variant of Concern 202012/01’ was published by PHE on Monday 21 December 2020

https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/947048/Technical_Briefing_VOC_SH_NJL2_SH2.pdf

https://www.gov.uk/government/publications/investigation-of-novel-sars-cov-2-variant-variant-of-concern-20201201

https://www.gov.uk/government/collections/new-sars-cov-2-variant

All our previous output on this subject can be seen at this weblink:

www.sciencemediacentre.org/tag/covid-19

Declared interests

None received.