January 1, 2021

expert reaction to the new Imperial pre-print on the new SARS-CoV-2 variant

A preprint, an unpublished non-peer reviewed study, posted by Imperial College London reports on the transmission of the new SARS-CoV-2 variant.

Dr Julian W Tang, Honorary Associate Professor/Clinical Virologist, University of Leicester, said:

“Some of these results from this Imperial College paper were released earlier – and a preprint from the LSHTM has also been released:

https://www.medrxiv.org/content/10.1101/2020.12.24.20248822v1

and another preprint from colleagues in Hong Kong:

https://www.medrxiv.org/content/medrxiv/early/2020/12/23/2020.12.20.20248581.full.pdf

both estimating similar increased rates of transmission (50-80%) with this new UK variant.

“In fact the use of the SGTF (S-gene target failure) by the Imperial College analysis likely underestimates the number of POS cases due to the new variant, as some labs (like ours) do not use any COVID-19 assays that target the S gene – exactly because we anticipated S gene mutations evolving over the course of the pandemic. So we are likely detecting new UK variant cases without identifying them as such (except via retrospective sequencing later) as we will not see this SGTF effect with our assays. There may be other labs like ours not using such S-gene target assays that may be underestimating this variant frequency also.

“It is still difficult to separate out human behavioural vs. viral genetic contributions as causes for enhanced transmissibility in all populations, but regardless, in practice, we just have to deal with this.

“Opening the Nightingale hospitals will help, but the problem is staffing them and equipping them adequately – given that staff in the mainstream NHS hospitals are already overworked and exhausted.

“These large second wave Christmas/post-Christmas and New Year surges were anticipated with the lead up to the festive season – though the new variant virus was not.

“The vaccine rollout is welcome news, but it is not likely to impact on the current surge in cases. So we really need to strictly follow our Tier restrictions, otherwise the virus will spread further to the vulnerable, who will require hospitalisation – which may further overwhelm existing NHS capacity in more sites.”

Dr Thomas House, Reader in Mathematical Statistics, University of Manchester, said:

“This is high quality work on the new variant, an issue that is still subject to considerable uncertainty. It involves a series of statistical analyses of multiple datasets with the aim of assessing increased transmissibility. Significant caution is required in the interpretation of these results due to the complexity of the data and models. Just because a range of values (e.g. “a reproduction number that is 0.4 to 0.7 higher”) is quoted, that does not mean that the analysis rules out, for example, much smaller changes in transmissibility. This is because the analysis may not account for a source of significant bias, or the methods used to calculate the range of values may be optimistic about uncertainty. In order to assess whether such a situation occurred, it is preferable for there to be independent verification of the results, which has not happened at this stage. It is also important not to over-interpret any small differences in age profile of new variant cases, which may also be due either to biases or uncertainty. Overall, this work adds to the evidence that the new variant is of concern, but we should expect the quantification of the level of concern to become more precise in the coming weeks.”

Prof Jim Naismith, Director of the Rosalind Franklin Institute, and Professor of Structural Biology, University of Oxford, said:

“It is not really possible to over state how serious this new strain is. The UK at a country level has not managed to hold R at 0.5 or below for any meaningful period. The data from Imperial represent the best analysis to date and imply that the measures we have employed to date, would with the new virus would fail to reduce the Rt to below 1. In simpler terms, unless we do something different the new virus strain is going to continue to spread, more infections, more hospitalisations and more deaths. The NHS is under serious strain and without a change this will get worse. January and early February will be difficult. If we fail to reduce the spread of the new strain, then we are likely to overwhelm the NHS, the consequences of this would be dire. 

“It should be noted that had we not had the November lockdown, we would most likely would have overloaded the NHS already. This lesson needs to be learned.”

Professor Lawrence Young,  Virologist and Professor of Molecular Oncology, University of Warwick, said:

“This preprint confirms that the new virus variant which is fuelling infections in the UK is more transmissible (infectious).

It highlights that this variant is responsible for the increased levels of infection observed in individuals under 20 years old.

This suggests that the spread of this virus variant during a period of lockdown may have been driven by schools remaining open.

There is no indication at this point of increased disease severity associated with the new variant. It is unlikely that this new variant will impact vaccine effectiveness but this is currently being investigated by the PHE.

“Variants of SARS-CoV-2 have been around since the beginning of the pandemic and are a product of the natural process by which viruses develop and adapt to their hosts as they replicate.  Most of these mutations have no effect on the behaviour of the virus but very occasionally they can improve the ability of the virus to infect and/or become more resistant to the body’s immune response.  Many thousands of these mutations have already been identified in isolates of the virus with around 4000 spike mutations being found in different viruses from around the world.  The UK and South African virus variants have changes in the spike gene consistent with the possibility that they are more infectious. 

“But the standard measures to restrict transmission (hands, face, space) will prevent infection with the UK and other variants.  Along with improved surveillance (testing, tracing and isolating) and expediating the roll out of vaccines, these measures will prevent transmission of this variant and any others that will arise.”  

Report 42 “Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: insights from linking epidemiological and genetic data” 

The full report can be downloaded here: https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/covid-19/report-42-sars-cov-2-variant/

Declared interests

None received.